Reciprocal subtraction differential display

ABSTRACT

This invention provides a method for identifying differentially expressed nucleic acids between two samples, comprising: a) selecting a first and second nucleic acid sample; b) producing libraries for the first and second nucleic acid sample; c) performing reciprocal subtraction between the libraries to produce two subtracted libraries; d) amplifying the two subtracted libraries; and e) comparing the two amplified subtracted libraries to identify differentially expressed nucleic acids. Also, this invention provides the above-described method, wherein the 3′ primer used in the PCR amplification is an oligo dT 3′ primer. This invention also provides the above-described methods, wherein the comparing of step e comprises using a gel to separate the nucleic acids from both of the libraries. This invention provides the isolated nucleic acid identified by the the above-described methods, wherein the nucleic was not previously known to be differentially expressed between the two samples.

[0001] This application is a continuation-in-part of U.S. Ser. No. 09/197,889, filed Nov. 23, 1998, which is a continuation-in-part of U.S. application Ser. No. 09/185,115, filed Nov. 3, 1998 which is a continuation-in-part of U.S. application Ser. No. 09/032,684, filed Feb. 27, 1998. The content of the above identified applications are hereby incorporated into this application by reference.

[0002] Throughout this application, various references are referred to within parentheses. Disclosures of these publications in their entireties are hereby incorporated by reference into this application to more fully describe the state of the art to which this invention pertains.

BACKGROUND OF THE INVENTION

[0003] Changes in gene expression are important determinants of normal cellular physiology, including cell cycle regulation, differentiation and development, and they directly contribute to abnormal cellular physiology, including developmental anomalies, aberrant programs of differentiation and cancer (1-4). In these contexts, the identification, cloning and characterization of differentially expressed genes will provide relevant and important insights into the molecular determinants of processes such as growth, development, aging, differentiation and cancer. A number of procedures can be used to identify and clone differentially expressed genes. These include, subtractive hybridization (5-10), differential RNA display (DDRT-PCR) (3,4, 11,12), RNA fingerprinting by arbitrarily primed PCR (RAP-PCR) (13,14), representational difference analysis (RDA) (15), serial analysis of gene expression (SAGE) (16,17), electronic subtraction (18,19) and combinatorial gene matrix analyses (20).

[0004] Since first introduced by Liang and Pardee (11), DDRT-PCR has gained wide popularity in analyzing and cloning differentially expressed genes. In DDRT-PCR, total RNAs or mRNAs from two or more cell types (or cells grown under different conditions, cells representing different stages of development, cells treated with agents modifying cellular physiology, etc.) are reverse-transcribed with two-base-pair anchored oligo dT primers, which divide mRNA populations into 12 cDNA subgroups. Then, each cDNA subgroup is amplified by PCR with one of 20 arbitrary 10-mer 5′ primers and a 3′ anchored primer and the PCR-amplified cDNA fragments are resolved in DNA sequencing gels. The combinations of primers are designed not only to yield a detectable size and number of bands, but also to display nearly the complete repertoire of mRNA species.

[0005] DDRT-PCR is a powerful methodology in which a vast number of mRNA species (>20,000, if no redundancy occurs) can be analyzed with only a small quantity of RNA (about 5 μg) (11). DDRT-PCR is often the method of choice when the RNA source is limiting, such as tissue biopsies. A direct advantage of DDRT-PCR is the ability to identify and isolate both up- and down-regulated differentially expressed genes in the same reaction. Furthermore, the DDRT-PCR technique permits the display of multiple samples in the same gel, which is useful in defining specific diagnostic alterations in RNA species and for temporally analyzing gene expression changes. However, the DDRT-PCR technique is not problem free. Difficulties encountered when using standard DDRT-PCR include, a high incidence of false positives and redundant gene identification, poor reproducibility, biased gene display and lack of functional information about the cloned cDNA. Furthermore, poor separation can mask differentially expressed genes of low abundance under the intense signals generated by highly expressed genes. The generation of false positives and redundancy can be highly problematic, resulting in an inordinate expenditure of resources to confirm appropriate differential expression and uniqueness of the isolated cDNAs. The cDNAs must be isolated from the gels in pure form (contamination of bands with multiple sequences complicates clone identification), reamplified, placed in an appropriate cloning vector, analyzed for authentic differential expression and finally sequenced. These limitations of the standard DDRT-PCR approaches emphasize the need for improvements in this procedure to more efficiently and selectively identify differentially expressed genes.

[0006] A number of modifications and improvements of the DDRT-PCR approach have been described (21-23). Single anchor or degenerate two-base anchor oligo dT primers can be used to streamline the massive numbers of reverse transcription and PCR reactions required for validation of cDNAs as well as to reduce false positives (24,25). Reproducibility can be improved by lengthening the arbitrary 5′ primers to accommodate a convenient restriction site followed by two cycles of PCR with successive low- and high-stringency annealing temperatures (25,26). DDRT-PCR with inosine-containing 5′ arbitrary primers can also increase reproducibility of this approach (27). However, since these modifications have only been analyzed using a subset of primers, further studies are necessary to validate these modifications of DDRT-PCR with additional primers and in several model systems.

[0007] In addition to genomic DNA contamination, mispriming, PCR artifacts, the high incidence of false positives and redundancy is also ascribed to poor separation between bands and the complexity of the templates amplified (28). Furthermore, poor separation can mask differentially expressed genes of low abundance under the intense signals generated by highly expressed genes. By enriching for unique cDNAs and removing common ones, it should in principle be possible to enrich for low abundant gene products and significantly decrease the complexity of amplified sequences. In addition, the sequence bias of DDRT-PCR should also be reduced by decreasing template complexity. These assumptions serve as the basis for the development of reciprocal subtraction differential RNA display (RSDD).

[0008] Subtractive hybridization, in which hybridization between tester and driver is followed by selective removal of common gene products, enriches for unique gene products in the tester cDNA population and reduces the abundance of common cDNAs (9). A subtracted cDNA library can be analyzed to identify and clone differentially expressed genes by randomly picking colonies or by differential screening (29-31). Although subtractive hybridization has been successfully used to clone a number of differentially expressed genes (5-7,10), this approach is both labor-intensive and does not result in isolation of the full spectrum of genes displaying altered expression (9,18).

[0009] In principle, DDRT-PCR performed with subtracted RNA or cDNA samples represents a powerful strategy to clone up and down-regulated gene products. This approach should result in the enrichment of unique sequences and a reduction or elimination of common sequences. This scheme should also result in a consistent reduction in band complexity on a display gel, thereby permitting a clearer separation of cDNAs resulting in fewer false positive reactions. Additionally, it should be possible to use fewer primer sets for reverse transcription and PCR reactions to analyze the complete spectrum of differentially expressed genes. Of particular importance for gene identification and isolation, rare gene products that are masked by strong common gene products should be displayed by using subtraction hybridization in combination with DDRT-PCR. In addition, the DDRT-PCR approach with subtractive libraries could also prove valuable for efficiently screening subtracted cDNA libraries for differentially expressed genes. However, even though subtraction hybridization plus DDRT-PCR appears attractive for the reasons indicated above, a previous attempt to use this approach has proven of only marginal success in consistently reducing the complexity of the signals generated, compared with the standard DDRT-PCR scheme (32).

[0010] We presently describe a reciprocal subtraction differential RNA display (RSDD) approach that efficiently and consistently reduces the complexity of DDRT-PCR and results in the identification and cloning of genes displaying anticipated differential expression.

SUMMARY OF THE INVENTION

[0011] This invention provides a method for identifying differentially expressed nucleic acids between two samples, comprising: (a) selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; (b) performing reciprocal subtraction between the nucleic acid samples to produce two subtracted nucleic acid samples; (c) amplifying the two subtracted nucleic acid samples; and (d) comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.

[0012] This invention also provides a method for identifying differentially expressed nucleic acids between two samples, comprising: (a) selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; (b) amplifying the two nucleic acid samples; (c) performing reciprocal subtraction between the amplified nucleic acid samples to produce two subtracted nucleic acid samples; and (d) comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.

[0013] This invention further provides the above-described methods, wherein the first and second nucleic acid samples are obtained from cells in different developmental stages.

[0014] This invention further provides the above-described methods, wherein the first and second nucleic acid samples are obtained from cells from different tissue types.

[0015] Also, this invention provides the above-described methods, wherein the 3′ primer used in the PCR amplification is an oligo dT 3′ primer.

[0016] In addition, this invention provides the above-described methods, wherein the 3′ primer used in the PCR amplification is a single anchor oligo dT 3′ primer.

[0017] This invention also provides the above-described methods, wherein the comparing of step (e) comprises using a gel to separate the nucleic acids from both of the libraries.

[0018] This invention provides the isolated nucleic acid identified by the the above-described methods, wherein the nucleic acid was not previously known to be differentially expressed between the two samples.

BRIEF DESCRIPTION OF THE FIGURES

[0019]FIG. 1 Identification of differentially expressed sequence tags using reciprocal subtraction differential RNA display (RSDD). Left panel: differential RNA display pattern of conventional DDRT-PCR with RNA from E11 (C) and E11-NMT (T) cells and an RSDD analysis of reciprocally subtracted E11 minus E11-NMT (C/T) and E11-NMT minus E11 (T/C) cDNA libraries. Right panel: representative RSDD patterns using different sets of primers.

[0020]FIG. 2 Reverse Northern analysis of differentially expressed sequence tags identified by reciprocal subtraction differential RNA display (RSDD). Differentially expressed sequence tags obtained from RSDD were dot-blotted onto Nylon membranes and probed with 32P-cDNA reverse transcribed from RNA samples of E11 and E11-NMT cells.

[0021]FIG. 3A Differential expression of representative progression elevated genes (PEGen) and progression suppressed genes (PSGen) identified by reciprocal subtraction differential RNA display (RSDD) and reverse Northern blotting. Northern blots of E11 and E11-NMT RNA samples were probed with radiolabeled (³²P) expressed sequence tags identified by RSDD and reverse Northern blotting.

[0022]FIG. 3B Differential expression of representative progression elevated genes (PEGen) and progression suppressed genes (PSGen) identified by reciprocal subtraction differential RNA display (RSDD) and reverse Northern blotting.

[0023]FIG. 4 Differential expression of representative progression elevated genes (PEGen) and progression suppressed genes (PSGen) identified by reciprocal subtraction differential RNA display (RSDD) and reverse Northern blotting. Northern blots of cells displaying various stages of transformation progression were probed with radiolabeled (³²P) expressed sequence tags identified by RSDD and reverse Northern blotting. The cell types used include, Unprogressed E11 (−), CREF×E11-NMT F1 (−) and CREF×E11-NMT F2 (−) somatic cell hybrids, E11×E11-NMT A6 (−) somatic cell hybrid, E11×E11-NMT 3b (−) somatic cell hybrid, and E11-NMT Aza B1 (−) and E11-NMT Aza C1 (−) 5-azacytidine treated E11-NMT clones; and Progressed E11-NMT (+), CREF×E11-NMT R1 (+) and CREF×E11-NMT R2 (+) somatic cell hybrids, E11×E11-NMT A6TD (+) nude mouse tumor derived somatic cell hybrid, E11×E11-NMT IIa (+), E11-Ras R12 (+) a Ha-ras transformed E11 clone and E11-HPV E6/E7 (+) an E11 clone transformed by the E6 and E7 region of HPV-18.

[0024]FIG. 5 cDNA fragment of PEGen 7—90% Homology to Human HPV16 E1BP. (Sequence ID No. 1)

[0025]FIG. 6 cDNA fragment of PEGen 8—Rat phosphofructose kinase C. (Sequence ID No. 2)

[0026]FIG. 7 First (Sequence ID No. 3) and second (Sequence ID No. 4) cDNA fragments of PEGen 13.

[0027]FIG. 8 cDNA fragment of PEGen 14. (Sequence ID No. 5)

[0028]FIG. 9 cDNA fragment of PEGen 15. (Sequence ID No. 6)

[0029]FIG. 10 cDNA fragment of PEGen 21 which has 94 homology to mouse FIN 14. (Sequence ID No. 7)

[0030]FIG. 11 cDNA fragment of PEGen 24. (Sequence ID No. 8)

[0031]FIG. 12 cDNA fragment of PEGen 26—Rat poly ADP-ribose polymerase. (Sequence ID No. 9)

[0032]FIG. 13 cDNA fragment of PEGen 28. (Sequence ID No. 10)

[0033]FIG. 14 cDNA fragment of PEGen 42. (Sequence ID No. 11)

[0034]FIG. 15 cDNA fragment of PEGen 43. (Sequence ID No. 12)

[0035]FIG. 16 cDNA fragment of PEGen 44. (Sequence ID No. 13)

[0036]FIG. 17 cDNA fragment of PEGen 48. (Sequence ID No. 14)

[0037]FIG. 18 cDNA fragment of PSGen 1 which has 80% homology to B. taurus supervillin. (Sequence ID No. 15)

[0038]FIG. 19 cDNA fragment of PSGen 2 which has 91% homology to human HTLV-1 Tax interacting protein. (Sequence ID No. 16)

[0039]FIG. 20 cDNA fragment of PSGen 4—Rat proteasome activator. (Sequence ID No. 17)

[0040]FIG. 21 cDNA fragment of PSGen 10—Rat Ferritin Heavy Chain. (Sequence ID No. 18)

[0041]FIG. 22 cDNA fragment of PSGen 12. (Sequence ID No. 19)

[0042]FIG. 23 cDNA fragment of PSGen 13. (Sequence ID No. 20)

[0043]FIG. 24 cDNA fragment of PSGen 23. (Sequence ID No. 21)

[0044]FIG. 25 cDNA fragment of PSGen 24. (Sequence ID No. 22)

[0045]FIG. 26 cDNA fragment of PSGen 25. (Sequence ID No. 23)

[0046]FIG. 27 cDNA fragment of PSGen 26.

[0047]FIG. 28 cDNA fragment of PSGen 27.

[0048]FIG. 29 cDNA fragment of PSGen 28.

[0049]FIG. 30 cDNA fragment of PSGen 29.

[0050]FIG. 31 cDNA fragment of PEGen 32.

[0051]FIG. 32 Schematic outline of the reciprocal differential RNA display (RSDD) protocol. This scheme incorporates three steps, reciprocal subtraction of cDNA libraries, differential display of in vivo excised cDNAs and expression analysis by reverse Northern and standard Northern blotting. For the present application of RSDD, reciprocal subtraction hybridization was performed using libraries constructed from E11 and E11-NMT cells, i.e., E11 minus E11-NMT and E11-NMT minus E11. Differentially expressed cDNAs identified on gels using differential RNA were isolated, reamplified and analyzed for expression by reverse Northern blotting. To confirm differential expression cDNAs were analyzed using Northern blotting.

[0052]FIG. 33 Differential expression of representative progression elevated (PEGen) and progression suppressed genes (PSGen) identified by RSDD and reverse Northern blotting. Northern blots of E11 and E11-NMT RNA samples were probed with radiolabeled (³²P) expressed sequence tags identified by RSDD and reverse Northern blotting. Equal loading of E11 and E11-NMT RNA is demonstrated by ethidium bromide (EtBr) Staining

[0053]FIG. 34 Differential expression of representative PEGen and PSGen genes identified by RSDD and reverse Northern blotting in a large panel of rodent cells displaying differences in transformation progression. Northern blots of cells displaying various stages of transformation progression were probed with radiolabeled (³²P) expressed sequence tags identified by RSDD and reverse Northern blotting. The cell types used include: Unprogressed E11 (-), CREF ×E11-NMT F1 (−) and CREF×E11-NMT F2 (−) somatic cell hybrids, E11×E11-NMT A6 (−) somatic cell hybrid, E11×E11-NMT 3b (−) somatic cell hybrid, and E11-NMT AZA B1 (−) and E11-NMT AZA C1 (−) 5-azacytidine-treated E11-NMT clones; and Progressed E11-NMT (+), CREF×E11-NMT R1 (+) and CREF×E11-NMT R2 (+) somatic cell hybrids, E11×E11-NMT A6TD (+) nude mouse tumor derived somatic cell hybrid, E11×E11-NMT IIa (+), E11-Ras R12 (+) and E11-HPV E6/E7 (+) an E11 clone transformed by the E6 and E7 region of HPV-18. Equal loading of RNAs is demonstrated by ethidium bromide (EtBr) staining.

[0054]FIG. 35A PSGen 12 cDNA Sequence and PSGen 12 Protein Sequence

[0055]FIG. 35B PSGen 13 cDNA Sequence and PSGen 13 Protein Sequence

[0056]FIG. 35C PEGen 28 cDNA Sequence and PEGen 28 Protein Sequence

[0057]FIG. 35D PEGen 32 cDNA Sequence and PEGen 32 Protein Sequence

[0058]FIG. 35E PEGen 42 cDNA Sequence and PEGen 42 Protein Sequence

[0059]FIG. 35F PEGen 45 cDNA Sequence

[0060]FIG. 35G-1 and FIG. 35G-2 PEGen 50 cDNA Sequence which are different parts of the gene.

[0061]FIG. 36 PSGen 27—Novel

DETAILED DESCRIPTION OF THE INVENTION

[0062] This invention provides a method for identifying differentially expressed nucleic acids between two samples, comprising: (a) selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; (b) performing reciprocal subtraction between the nucleic acid samples to produce two subtracted nucleic acid samples; (c) amplifying the two subtracted nucleic acid samples; and (d) comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.

[0063] In an embodiment, the nucleic acid samples are mRNA or derived from mRNA. In another embodiment, the nucleic acid samples are total RNA. In another embodiment, the nucleic acid samples are cDNA. In another embodiment, the nucleic acid samples are a nucleic acid library.

[0064] In an embodiment, differentially expressed nucleic acids are expressed at different levels. In a further embodiment, one of the nucleic acids is not expressed. In a different embodiment, one of the nucleic acids is expressed in truncated form.

[0065] As used herein, reciprocal subtraction includes using nucleic acid sample A to subtract common nucleic acids from nucleic acid sample B (based on hybridization) and also using nucleic acid sample B to subtract common nucleic acids from nucleic sample A. In an embodiment, the complement of nucleic acid sample A is used to subtract nucleic acids from nucleic acid sample B and the complement of nucleic acid sample B is used to subtract nucleic acids from nucleic acid sample A. In a further embodiment, the RNA of nucleic acid sample A is used to subtract nucleic acids from nucleic acid sample B and the RNA of nucleic acid sample B is used to subtract nucleic acids from nucleic acid sample A. In yet another embodiment, the cDNA of nucleic acid sample A is used to subtract nucleic acids from nucleic acid sample B and the cDNA of nucleic acid sample B is used to subtract nucleic acids from nucleic acid sample A.

[0066] As used herein, methods of amplification include PCR and rolling circle replication.

[0067] A basic description of nucleic acid amplification is described in Mullis, U.S. Pat. No. 4,683,202, which is incorporated herein by reference. The amplification reaction uses a template nucleic acid contained in a sample, two primer sequences and inducing agents. The extension product of one primer when hybridized to the second primer becomes a template for the production of a complementary extension product and vice versa, and the process is repeated as often as is necessary to produce a detectable amount of the sequence.

[0068] The inducing agent may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Suitable enzymes for this purpose include, for example, E. coli DNA polymerase I, thermostable Taq DNA polymerase, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, reverse transcriptase and other enzymes which will facilitate combination of the nucleotides in the proper manner to form amplification products. The oligonucleotide primers can be synthesized by automated instruments sold by a variety of manufacturers or can be commercially prepared based upon the nucleic acid sequence of this invention.

[0069] This invention also provides a method for identifying differentially expressed nucleic acids between two samples, comprising: a) selecting a first and second nucleic acid sample; b) producing libraries for the first and second nucleic acid sample; c) amplifying the two libraries; d) performing reciprocal subtraction between the amplified libraries to produce two subtracted libraries; and e) comparing the two subtracted libraries to identify differentially expressed nucleic acids.

[0070] This invention also provides a method for identifying differentially expressed nucleic acids between two samples, comprising: (a) selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; (b) amplifying the two nucleic acid samples; (c) performing reciprocal subtraction between the amplified nucleic acid samples to produce two subtracted nucleic acid samples; and (d) comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.

[0071] This invention also provides the above-described methods, wherein the two subtracted nucleic acid samples from step c are amplified prior to the comparing of step d.

[0072] This invention also provides the above-described methods, wherein the each of the nucleic acid samples comprises a library of nucleic acids.

[0073] This invention also provides the above-described methods, wherein the nucleic acid samples are obtained from total cellular RNA purified by hybridization with oligo (dT).

[0074] This invention also provides the above-described methods, wherein the nucleic acid samples are obtained from total RNA from E11 and E11-NMT cells.

[0075] E11 is an adenovirus-transformed rat embryo cell line that acquires an aggressive oncogenic progression phenotype when injected into athymic nude mice and reisolated in cell culture (E11-NMT).

[0076] This invention further provides the above-described methods, wherein the first and second nucleic acid samples are obtained from cells in different developmental stages.

[0077] This invention further provides the above-described methods, wherein the first and second nucleic acid samples are obtained from cells from different tissue types.

[0078] This invention further provides the above-described methods, wherein the first and second nucleic acid samples are obtained from cells that differ in their exposure to external factors or in their gene expression.

[0079] In an embodiment, cells that differ in their exposure to external factors or in their gene expression includes any cells that may have different levels of gene expression, wherein some genes may not be expressed at all. In another embodiment, cells that differ in their exposure to external factors or in their gene expression includes any cells that are likely to have different levels of gene expression, wherein some genes may not be expressed at all. In still another embodiment, cells that differ in their exposure to external factors or in their gene expression includes any cell that has a phenotypically recognizable difference.

[0080] A short list of examples of cells that differ in their exposure to external factors or in their gene expression includes: cancerous versus normal cells, advanced cancer progression cells versus ealier cancer stage cells, diseased cells versus nondiseased cells, infected cells versus noninfected cells, later developmental stage cells versus earlier developmental stage cells, cells after DNA damage versus cells before DNA damage, senescent cells versus younger cells, cells induced by growth factors versus cells not induced by growth factors, cells in the process of neurodegeneration versus normal cells, and cells exposed to a chemotherapeutic agent versus normal cells.

[0081] As used herein, different tissues types include but are not limited to tissues containing: cells grown under or exposed to different conditions, cells in different stages of development, cells treated with agents modifying cellular physiology, and cells having different functions.

[0082] In an embodiment, cells at different stages of development are cells taken or analyzed at times differing by one or more hours in the development of the cell or organism.

[0083] Further, this invention provides the above-described methods, wherein the amplifying of step (d) comprises PCR amplification.

[0084] Also, this invention provides the above-described methods, wherein the 3′ primer used in the PCR amplification is an oligo dT 3′ primer. A few examples of oligo dT primers are T₁₃, T₁₃A, and T₁₃GA.

[0085] In addition, this invention provides the above-described methods, wherein the 3′ primer used in the PCR amplification is a single anchor oligo dT 3′ primer. olgio dT 3′ primers include T₁₃A, T₁₃C, and T₁₃G.

[0086] This invention provides the above-described methods, wherein the PCR amplification uses a set of random primers.

[0087] This invention provides the above-described methods, wherein the 5′ primer is an arbitrary primer.

[0088] This invention also provides the above-described methods, wherein the comparing of step (e) comprises using a gel to separate the nucleic acids from both of the substracted libraries.

[0089] In an embodiment, the gel is a polyacrylamide gel. In another embodiment, the gel is an agarose gel.

[0090] This invention further provides the above-described methods, further comprising PCR amplifying the first and second nucleic acid samples.

[0091] This invention also provides the above-described methods, further comprising reamplifying differentially expressed bands.

[0092] This invention also provides the above-described methods, further comprising reamplifying differentially expressed nucleic acid.

[0093] In one method of reamplifying differentially expressed bands, differentially amplified bands from plasmids of each subtracted library were marked with an 18 G needle through the film and cut out with a razor. The cut out differentially expressed bands can be reamplified (i.e. by PCR) and examined by reverse Northern and Northern blot analyses.

[0094] In addition, this invention provides the above-described methods, wherein the comparing of step (e) comprises comparing the band intensities of the two amplified differentially expressed nucleic acids.

[0095] In addition, this invention provides the above-described methods, wherein the nucleic acid samples are mRNA or cDNA derived from mRNA.

[0096] In addition, this invention provides the above-described methods, wherein the comparing of step (e) comprises comparing the quantities of the two amplified differentially expressed nucleic acids.

[0097] This invention further provides the above-described methods, wherein the differences in band intensity between the two subtracted libraries are electronically quantified.

[0098] This invention further provides the above-described methods, wherein the differences in the quantities of nucleic acid between the two subtracted libraries are electronically quantified.

[0099] In one embodiment, electronic quantification involves using a scanner to detect the bands. In a further embodiment, computer software, such as Corel Draw, can be used to determine the pixel intensity of the scanned image, thereby quantifying the band intensity.

[0100] Also, this invention provides the above-described methods, wherein the libraries of step (b) are constructed with λ-ZAP cDNA library kits. One skilled in the art would recognize that any cDNA library would be suitable.

[0101] This invention provides the isolated nucleic acid identified by the the above-described methods, wherein the nucleic acid was not previously known.

[0102] This invention also provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 12 (AI 144569).

[0103] In addition, this invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 13 (Accession No. AI 144570).

[0104] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 23.

[0105] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 24.

[0106] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 25.

[0107] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 26 (Accession No. AI 144571).

[0108] This invention also provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 27 (Accession No. AI 144572).

[0109] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 28 (AI 144573).

[0110] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PSGen 29 (AI 144574).

[0111] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 13 (AI 144564).

[0112] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 14 (AI 144565).

[0113] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 15.

[0114] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 24 (Accession No. AI 144566).

[0115] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 28 (AI 144567).

[0116] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 32 (AI 144568).

[0117] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 42.

[0118] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 43.

[0119] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 44.

[0120] This invention provides the above-described isolated nucleic acid, wherein the isolated nucleic acid is the nucleic acid designated PEGen 48.

[0121] This invention further provides a previously unknown isolated nucleic acid molecule identified by the above-described methods which comprises (a) one of the nucleic acid sequences as set forth in FIG. 35; (b) a sequence being degenerated to a sequence of (a) as a result of the genetic code; (c) a sequence encoding one of the amino acid sequences as set forth in FIG. 35. (d) a sequence of at least 12 nucleotides capable of specifically hybridizing to the sequence of (a), (b) or (c).

[0122] Finally, this invention provides a purified polypeptide comprising one of the amino acid sequence as set forth in FIG. 35.

[0123] The sequences of the cDNA of PSGen 12, PSGen 13, PSGen 26, PSGen 27, PSGen 28, PSGen 29, PEGen 13, PEGen 14, PEGen 24, PEGen 28, and PEGen 32 were submitted to GenBank and assigned with accession numbers AI 144569, AI 144570, AI 144571, AI 144572, AI 144573, AI 144574, AI 144564, AI 144565, AI 144566, AI 144567 and AI 144568 respectively.

[0124] This invention will be better understood from the Experimental Details which follow. However, one skilled in the art will readily appreciate that the specific methods and results discussed are merely illustrative of the invention as described more fully in the claims which follow thereafter.

[0125] Experimental Details

[0126] We presently describe a reciprocal subtraction differential RNA display (RSDD) approach that efficiently and consistently reduces the complexity of DDRT-PCR and results in the identification and cloning of genes displaying anticipated differential expression. Proof of principle for the RSDD approach has come from its application for the identification of genes differentially expressed during cancer progression. RSDD has resulted in the identification and cloning of genes displaying elevated expression in progressed tumor cells (PEGen) and reduced expression in progressed tumor cells (PSGen). The model used for RSDD was an adenovirus-transformed rat embryo cell line, E11, that acquires an aggressive oncogenic progression phenotype when injected into athymic nude mice and reisolated in cell culture (E11-NMT) (10,33,34). Injection of E11 cells into nude mice results in tumors in 100% of animals with a tumor latency time of approximately 35 to 40 days, whereas E11-NMT cells form tumors in 100% of nude mice with a tumor latency time of 15 to 20 days (10,34,35). Additionally, E11 cells form colonies in agar with an efficiency of ^(˜)3%, whereas E11-NMT display an agar cloning efficiency of >30% (10,33,34). The increased tumorigenicity and enhanced anchorage independence phenotypes are key indicators of tumor progression in the E11/E11-NMT model system (10,33,34).

[0127] Differential RNA display was directly performed with reciprocally subtracted cDNA plasmid libraries (E11 minus E11-NMT and E11-NMT minus E11). Compared with the subtraction of PCR-amplified cDNA in Hakvoort et al., the subtracted cDNA libraries used in this experiment are free from potential PCR artifacts and provide more stable and consistent sources for DDRT-PCR analyzes. In addition, three single anchored oligo dT 3′ primers were used instead of two-base-anchored approach described by Hakvoort et al (32). To further streamline the DDRT-PCR procedure, reamplified cDNAs identified using RSDD were analyzed using the reverse Northern blotting procedure (35,36). cDNAs displaying differential expression by reverse Northern blotting were subsequently confirmed for true differential expression by Northern analysis. These modifications incorporated in the RSDD strategy result in an efficient approach for using subtractive. hybridization and DDRT-PCR for identifying differentially expressed genes.

[0128] Methods

[0129] Total RNA from E11 and E11-NMT cells was isolated by the guanidinium isothiocyanate/CsCl centrifugation procedure and poly A⁺ RNA was purified with oligo(dT) cellulose chromatography (5). Two λ-ZAP cDNA libraries from E11 and E11-NMT mRNA's were constructed with λ-ZAP cDNA library Kits (Stratagene) following the manufacturer's protocol. Reciprocal subtraction between E11 and E11-NMT libraries was performed and two subtracted cDNA libraries (E11 minus E11-NMT and E11-NMT minus E11) were constructed as described previously. Bacterial plasmid libraries from the subtracted λ-ZAP cDNA libraries were obtained by in vivo excision following the manufacturer's protocol (Stratagene) and the plasmids were isolated with Qiagen columns (Qiagen Inc.).

[0130] The purified plasmids of reciprocally subtracted cDNA libraries were directly subjected to differential display as in Liang et. al. (38) with minor modifications. The plasmids of reciprocally subtracted cDNA libraries were PCR-amplified with the combination of three single-anchor 3′ primers (T₁₃ A, T₁₃ C or T₁₃ G) and 18 arbitrary 5′ 10-mer primers obtained from Operon Technology Inc. (Alameda, Calif. OPA1-20 except OPA1 and 3). The 20 μl PCR reaction consisted of 10 mM Tris-HCl pH 8.4, 50 mM KCl, 1.5 mM MgCl₂, 2 μM each dNTP, 0.2 μM 5′ arbitrary primer, 1 μM 3′ anchor primer, 50 ng of plasmid of a subtracted library, 10 μCi α-³⁵S-DATP (3000 Ci/mmole from Amersham) and 1 U of Taq DNA polymerase (Gibco BRL). The parameters of PCR were 30 sec at 95 C., 40 cycle of 30 sec at 95 C, 2 min. at 40 C. and 30 sec at 72 C. and additional 5 min. at 72 C. After the cycling, 10 μl of 95% formamide, 0.05% bromophenol blue and 0.05% xylene cyanol were added to each PCR reaction. The mixture was heated at 95° C. for 2 min and separated in a 5 denaturing DNA sequencing gel maintained at 50° C. PCR reactions of plasmids from each subtracted library in a primer set were run side by side. Differentially amplified bands from plasmids of each subtracted library were marked with an 18 G needle through the film and cut out with a razor. The gel slice was put in 100 μl TE pH 8.0 and incubated at 4° C. overnight. After the incubation, the mixture was boiled for 5 min and microcentrifuged for two min. The supernatant was collected and stored at −20° C. until reamplification. The band extract was reamplified with the same cycling parameters in a 50 μl reaction consisting of 10 mM Tris-HCl pH 8.4, 50 mM KCl, 1.5 mM MgCl₂, 20 μM each dNTP, 0.2 μM 5′ arbitrary primer, 1 μM 3′ anchor primer, 5 μl of band extract and 2.5 U of Taq DNA polymerase (Gibco BRL).

[0131] Differential expression of the reamplified DNA fragment was scrutinized by reverse Northern and Northern blot analyses. In reverse Northern analysis, after confirmation in a 1% agarose gel, the reamplified DNA fragment (10 μl of PCR reaction) was mixed with 90 μl TE and spotted on a positively charged Nylon membrane (Boehringer Mannheim) with a 96-well vacuum manifold. The membrane was soaked with denaturing and neutralizing solution successively, and the spotted DNA was crosslinked to the membrane with a UV crosslinker (Stratagene). ³²P-labeled first strand cDNA was prepared by reverse transcription of total RNA. After heating at 70° C. for 10 min and quenching on ice for two min, 0.4 μM each T₁₃ A, T₁₃ G and T₁₃ C and 10 μg total RNA mixture was added with 50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.02 mM dCTP, 0.5 μl RNase inhibitor (Gibco BRL), 100 μCi dCTP (3000 Ci/mmole from Amersham) and 200 U Superscript RT II (Gibco BRL) in a final 25 μl reaction. The reaction mixture was incubated at 42° C. for one hr and at 37° C. for 30 min after addition of 2 μl of RNase H (10 U, Gibco BRL). The membrane was hybridized at 42° C. overnight in a 50% formamide hybridization solution. The hybridized membrane was washed at room temperature for 15 min with 2×SSC containing 0.10 SDS twice and at 55° C. for at least one hr with 0.1×SSC containing 0.1% SDS, successively. The membrane was probed with the ³²P-labeled cDNA of E11, stripped off and probed with ³²P-labeled cDNA of E11-NMT. The signal intensity of each spot was normalized against that of GAPDH and compared between E11 and E11-NMT. Reamplified DNA fragments displaying differential expression levels ≧1.8-fold higher between the two cell types were selected and analyzed by Northern blotting analysis.

[0132] In Northern blot analysis, 10 μg of total RNA from E11 and E11-NMT cells were run side-by-side in a 1% agarose gel with formaldehyde and transferred to a positively charged Nylon membrane. Reamplification reaction (5 μl) was ³²P-labeled with a multiprime labeling kit (Boehringer Mannheim) used to probe the membrane as described above. DNA fragments expressed differentially between E11 and Eil-NMT in Northern blot analyses were cloned into the Eco RV site of the pZEro-2.1 cloning vector (Invitrogene) and sequenced. In order to confirm differential expression, the cloned cDNA fragment was released by Eco RI -Xho I, ³²P-labeled and used to probe Northern blots as described above. Samples of RNAs from various E11 and E11-NMT derivatives displaying either a progressed or suppressed progression phenotype, based on nude mice tumorigenesis and soft agar cloning assays were analyzed. These included E11, E11-NMT, CREF×E11-NMT F1 and F2 somatic cell hybrids (suppressed progression phenotype), CREF×E11-NMT R1 and R2 somatic cell hybrids (progression phenotype), E11×E11-NMT A6 somatic cell hybrid (suppressed progression phenotype), E11×E11-NMT A6TD tumor-derived somatic cell hybrid (progression phenotype), E11×E11-NMT 3b somatic cell hybrid (suppressed progression phenotype), E11×E11-NMT 2a (progression phenotype), E11-NMT AZA B1 and C1 5-azacytidine treated E11-NMT clones (suppressed progression phenotype), E11-ras R12 clone containing the Ha-ras oncogene (progression phenotype) and E11-HPV E6/E7 clone containing the human papilloma virus-18 E6 and E7 gene region (progression phenotype). Differential expression of the PEGen and PSGen genes in the various cell types was confirmed using ³²P-labeled probes and Northern hybridization analysis. After reconfirmation of differential expression, the plasmids containing the differentially expressed DNA fragments were sequenced by the dideoxy sequencing procedure.

[0133] Results and Discussion

[0134] Subtraction hybridization provides a direct means of enriching for unique cDNA species and eliminating common sequences between complex genomes. DDRT-PCR is a proven methodology for the rapid identification and cloning of differentially expressed sequences between cell types (3,4,22). In principle, subtraction hybridization combined with DDRT-PCR should reduce band complexity which often obscures the identification of differentially expressed genes and generates false positive signals (23,28). This strategy, RSDD, has been used to analyze genes differentially expressed during transformation progression. The differential RNA display pattern of E11 and E11-NMT cells using standard differential RNA display DDRT-PCR) and RSDD is shown in FIG. 1 (Left Panel). As predicted, the differential RNA display pattern of RSDD was much less complex than that of DDRT-PCR. The majority of bands common to both cDNA samples were eliminated using RSDD. These experiments demonstrate that subtractive hybridization prior to differential RNA display is effective in simplifying display patterns permits the efficient identification of differentially expressed cDNAs. Since RSDD significantly reduced the number of bands displayed, single anchor oligo dT primers, that can increase band numbers, were successfully used in subsequent applications of the RSDD approach (FIG. 1; Right Panel). Using RSDD, 235 differentially displayed cDNAs in the E11/E11-NMT tumor progression model system were isolated.

[0135] Hakvoort et. al. (32) used a reciprocal subtraction approach to analyze gene expression changes resulting during liver regeneration following 70% hepatectomy, i.e., normal liver subtracted from partially hepatectomized regenerating liver and vice versa. Although some bands displayed apparent enrichment, the complexity of the display pattern did not show appreciable simplification. These results are in stark contrast to RSDD, which results in a clear delineation and simplification of differentially expressed amplified bands (FIG. 1). Although conceptually similar, RSDD is significantly more effective than the subtraction plus DDRT-PCR approach described by Hakvoort et al. (32). The improved efficiency of RSDD versus the Hakvoort et al. (32) approach can be attributed to several factors. The approach of Hakvoort et al. (32) is based on the subtraction procedure described by Wang and Brown (38). This approach involves multiple rounds of PCR-amplification prior to each round of subtractive hybridization. In contrast, RSDD involves a single round of reciprocal subtraction that does not involve PCR amplification (5,10). In this respect, the complicated display pattern observed by Hakvoort et al. (32) even after three or four rounds of subtraction might result from reduced subtraction efficiency, PCR artifacts or a combination of these problems. Increasing the number of reactions by using two-base pair anchored oligo dT primers did not reduce the complexity of displayed bands (32). In these contexts, a critical component for the successful use of RSDD involves the use-of an appropriate subtraction hybridization protocol, that can efficiently reduce cDNA complexity and generate stable populations of cDNAs for analysis.

[0136] Previous studies demonstrate that different gene cloning strategies, including DDRT-PCR, subtraction hybridization and electronic display, identify dissimilar differentially expressed genes (18). These results suggest that a single approach for gene identification may not identify the complete spectrum of differentially expressed genes (18). Similarly, RSDD and DDRT-PCR do not resolve the same differentially expressed bands (FIG. 1). Unique bands identified in DDRT-PCR that were differentially expressed when analyzed by Northern blotting were not the same as those found using RSDD and vise versa. These results are not surprising, since, as indicated above, subtraction hybridization and differential RNA display identified distinct differentially expressed genes. Apparently, specific differentially expressed genes are lost during subtraction hybridization and differential RNA display of subtracted cDNAs. On the basis of these considerations, it will be essential to use multiple gene discovery approaches to identify and clone the complete spectrum of differentially expressed genes.

[0137] DDRT-PCR can generate large numbers of differentially displayed bands making subsequent analysis both labor intensive and a daunting challenge. In order to reduce these limitations of DDRT-PCR, RSDD has been used in combination with reverse Northern analyses of isolated cDNAs. Gel extracted cDNA fragments were reamplified, dot-blotted on Nylon membranes and successively probed with reverse transcribed ³²P-cDNA from E11 or E11-NMT RNAs (FIG. 2). Signals were detected in 181 reamplified bands out of 235 (77%). This number is lower than that observed using DDRT-PCR (51 out of 54). However, this comparison may not be accurate since only four arbitrary primers were used for DDRT-PCR and fewer differentially expressed bands were detected and isolated. A possible reason for the high incidence of false positives in RSDD may be due to the existence of foreign plasmid-like DNA in the cDNAs and the inaccurate reading properties of DDRT-PCR. TABLE 1 Differentially Expressed cDNA Fragments Cloned by DDRT-PCR. Nomenclature Identity Homology PEGen 41 To be determined PEGen 42 Novel Novel PEGen 43 Novel Novel PEGen 44 Novel Novel PEGen 45 Hoxall locus antisense mouse 90% PEGen 46 Glutamyl t-RNA synthetase human 59% PEGen 48 Novel Novel PEGen 50 Novel Novel PSGen 1 Supervillin B. taurus 80% PSGen 2 HTLV-1 Tax interacting human 91% protein PSGen 4 Proteasome activator Rat 100% PSGen 27 Novel

[0138] The signal intensities of the various cDNAs in reverse Northern analysis were quantified and normalized against that of GAPDH, which remained unchanged in E11 and E11-NMT cells. The PEG-3 (PEGen-3) gene (10) was used as an additional control, to verify increased expression in E11-NMT versus E11 cells. In the reverse Northern analyses, PEGen-3 levels were 4-fold higher in E11-NMT than in E11 cells, which coincided with Northern blotting results, thereby demonstrating the concordance of reverse Northern and Northern assays. A≧1.8-fold differential cut-off (after normalization for GAPDH expression) was used to identify and isolate cDNA bands displaying modified expression in E11 versus E11-NMT cells. This resulted in the identification of 7 cDNAs with higher expression in E11 versus E11-NMT cells and 65 cDNAs with elevated expression in E11-NMT versus E11 cells. These results suggest that tumor progression in E11-NMT cells correlates with the increased expression of a large number of genes, whereas only a smaller subset of genes display decreased expression.

[0139] A problem present in DDRT-PCR, that is reduced but still can occur in RSDD, is the isolation of multiple cDNA species from what appears to be a single amplified band. When this occurs, these multiple species can produce spurious results when analyzed by reverse Northern analyses. For example, if two distinct species are isolated, one displaying modified expression and a second not displaying modified expression, an accurate estimate of differential expression will not be obtained by reverse Northern analysis. In this case, a number of potential false positives generated using reverse Northern analyses, may in reality not be false positives, but instead may represent multiple cDNAs. This problem may be ameliorated by performing single strand conformational polymorphism (SSCP) or reverse Northern analyses using cloned cDNA populations (39,40).

[0140] The expression pattern of representative RSDD-derived cDNAs in E11 versus E11-NMT and in a more expanded E11/E11-NMT progression cell culture series is shown in FIGS. 3 and 4, respectively. Reverse Northern results correlated well with Northern blots using E11 and E11-NMT (^(˜)80% concordance) or a larger panel of cells differentially displaying the progression phenotype, including progression negative, E11, CREF×E11-NMT F1, CREF×E11-NMT F2, E11×E11-NMT A6, E11×E11-NMT 3b, E11-NMT Aza B1 and E11-NMT Aza C1, and progression positive E11-NMT, CREF×E11-NMT R1, CREF×E11-NMT R2, E11×E11-NMT A6TD, E11×E11-NMT IIa, E11-ras and E11-HPV E6/E7. Sequence analysis of the various progression upregulated genes (PEGen) and progression suppressed genes (PSGen) identified both known and unknown genes (Table 2). Known PEGen genes included PEGen 7 (HPV16 ElBP), PEGen 8 (PFK-C), PEGen 21 (FIN 14) and PEGen 26 (poly ADP-ribose polymerase) and a known PSGen gene was PSGen 10 (ferritin heavy chain). Two PEGen genes out of six were found to be novel (PEGen 14 and PEGen 24) and two PSGen genes out of three were found to be novel (PSGen 12 and PSGen 13) (Table 2). TABLE 2 Differentially Expressed cDNA Fragments Cloned by RSDD Nomenclature Identity Homology PEGen 7 HPV16 E1BP Human 90% PEGen 8 PFK-C Rat 100% PEGen 13 Novel Novel PEGen 14 Novel Novel PEGen 15 Novel Novel PEGen 21 FIN 14 Mouse 94% PEGen 24 Novel Novel PEGen 26 Poly ADP-ribose Polymerase Rat 100% PEGen 28 Novel Novel PEGen 32 Novel Novel PSGen 10 Ferritin Heavy Chain Rat 100% PSGen 12 Novel Novel PSGen 13 Novel Novel PSGen 23 Novel Novel PSGen 24 Novel Novel PSGen 25 Novel Novel PSGen 26 Novel Novel PSGen 27 Novel Novel PSGen 28 Novel Novel PSGen 29 Novel Novel

[0141] PEGen 7 is expressed at ^(˜)5-fold higher levels in E11-NMT than in E11 cells. PEGen 7 is ^(˜)90% homologous to 16E1-BP, a cDNA encoding a protein identified using the yeast two-hybrid assay that interacts with human papillomavirus type 16 El protein (41). 16E1-BP encodes a 432aa protein of unknown function but does contain an ATPase signature motif (Gly-X₄-Gly consensus ATP binding motif at aa 179 through 186). 16E1-BP appears to be a form of TRIP13, a protein previously shown to bind thyroid hormone receptor in yeast two-hybrid assays. The role of PEGen {fraction (7/16)}E1-BP in the progression phenotype in the E11/E11-NMT progression model is not known. Additional studies are necessary to determine if this gene change is associative or causative of transformation progression.

[0142] PEGen 8 is expressed at ^(˜)3- to 4- fold higher levels in E11-NMT than in E11 cells. PEGen 8 shows 100% homology to rat phosphofructokinase C (PFK-C) (42). PFK catalyzes the rate-limiting and committed step in glycolysis, the conversion of fructose 6-phosphate to fructose 1,6-biphosphate. Three subunit isozymes of PFK have been identified, that form homo- and heterotetramers with differing catalytic and allosteric properties. PFK-M is specific for cardiac and skeletal muscle, PFK-L is expressed in many tissues but is most abundant in the liver and PFK-C is expressed in several brain regions and the anterior pituitary but not in liver, skeletal muscle, or several other human tissues. The cDNA of PFK-C isolated from a rat hypothalamic cDNA library is 2643 bp and encodes a protein of 765aa (42). In a recent study, Sanchez-Martinez and Aragon (43) demonstrated that PFK-C is the predominant form of PFK in ascites tumor cells (obtained from a transplantable mouse carcinoma of mammary origin), whereas PFK-L is most abundant in the normal mammary gland. These results suggest the interesting possibility that PFK-C might contribute to the malignant nature of specific target cells. The role of PEGen 8/PFK-C in progression in the E11/E11-NMT model remains to be determined.

[0143] PEGen 21 is expressed at ^(˜)3- to 4-fold higher levels in E11-NMT than in E11 cells. PEGen 21 displays ^(˜)94% homology with the fibroblast growth factor-4 inducible gene FIN-14 (44). FIN-14 is a novel cDNA of unknown function that hybridizes with a 4.5 kb mRNA that is induced 4-fold in NIH3T3 mouse cells following treatment with FGF-4. The induction of FIN-14 occurs late (18 hr) after treatment with FGF-4 and does not occur when cells are treated for 18 hr with FGF-4 in the presence of cycloheximide (44). These results confirm that FIN-14 encodes a late-inducible gene. Moreover, nuclear run-on assays document that FIN-14 is trancriptionally activated in NIH3T3 cells following growth factor stimulation. Tissue distribution studies indicate expression of a single mRNA species in the kidney with low levels of expression observed in several other tissues including testis and thymus. Mouse embryogenesis studies indicate that FIN-14 expression occurs constitutively in mouse embryos between day 10.5 and 15.5. Unlike NIH3T3, FIN-14 was constitutively expressed in PC12 cells and its level did not vary appreciably in response to growth factor stimulation. The role of PEGen 21/FIN-14 in progression in E11/E11-NMT model system is not currently known.

[0144] The PSGen cDNAs, PSGen-12 and PSGen-13, consist of sequences without homology to those presently reported in various DNA databases. Expression of these cDNAs is ^(˜)3- to 4-fold higher in E11 versus E11-NMT cells (FIG. 3). It is not currently known whether these genes simply correlate with or functionally regulate the progression phenotype. The identification of full-length cDNAs for PSGen-12 and PSGen-13 are in progress and once identified experiments can be conducted to directly define the role of these PSGen's in cancer progression.

[0145] We presently demonstrate that a modified differential RNA display technique, RSDD, can efficiently identify differentially expressed cDNAs. As predicted, subtractive hybridization prior to differential RNA display greatly reduces band complexity, a problem encountered in standard DDRT-PCR in which RNA samples are directly analyzed without subtraction. Unlike a previous report using subtracted cDNAs processed through successive rounds of PCR (32,45), common bands were eliminated using reciprocally subtracted cDNA libraries that had not been processed using PCR. In addition to subtraction hybridization, the discovery of differentially expressed genes was further streamlined by using reverse Northern analyses with isolated cDNAs. With 3 single anchored oligo dT primers and 18 arbitrary 5′ primers, 72 bands were identified that displayed differential expression using reverse Northern analysis. Currently, 40 of these cDNA species have been analyzed by Northern blotting and found to display differential expression in E11 versus E11-NMT cells. Subsequent studies with the majority of these RSDD cDNAs demonstrated coordinated expression with the progression phenotype in a large panel of unprogressed and progressed transformed cells. Current sequence analysis of the cloned cDNA fragments revealed 9 different genes, including 4 novel genes not reported in recent DNA databases. RSDD represents a method of choice either as a more efficient and less time consuming modification of the differential RNA display strategy or as a screening methodology for identifying differentially expressed genes in reciprocally subtracted cDNA libraries.

[0146] References For The First Series Of Experiments

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[0192] Second Series of Experiments

[0193] Presently described is a RSDD approach that efficiently and consistently reduces the complexity of DDRT-PCR and results in the identification and cloning of genes displaying anticipated differential expression. The model used for RSDD was an adenovirus-transformed rat embryo cell line, E11, that acquires an aggressive oncogenic progression phenotype when injected into athymic nude mice and reestablished in cell culture (E11-NMT) (6,26,27). Injection of E11 cells into nude mice results in tumors in 100% of animals with a tumor latency time of approximately 35 to 40 days, whereas E11-NMT cells form tumors in 100% of nude mice with a tumor latency time of 15 to 20 days (6,26,27). Additionally, E11 cells form colonies in agar with an efficiency of ^(˜)3 %, whereas E11-NMT display an agar cloning efficiency of >30% (6,26,27). The increased tumorigenicity and enhanced anchorage independence phenotypes are key indicators of tumor progression in the E11/E11-NMT model system (6,26,27). RSDD has resulted in the identification and cloning of genes displaying elevated expression in progressed tumor cells (progression elevated gene, PEGen) and suppressed expression in progressed tumor cells (progression suppressed gene, PSGen).

[0194] Materials and Methods

[0195] RNA isolation and cDNA library construction. Total RNA from E11 and E11-NMT cells was isolated by the guanidinium isothiocyanate/CsCl centrifugation procedure and poly(A)⁺ RNA was purified with oligo(dT) cellulose chromatography(5). Two λ-ZAP cDNA libraries from E11 and E11-NMT mRNAs were constructed with λ-ZAP cDNA library kits (Stratagene) following the manufacturer's protocol. Reciprocal subtraction between E11 and E11-NMT libraries was performed and two subtracted cDNA libraries (E11 minus E11-NMT and E11-NMT minus E11) were constructed as described(5,6). Plasmid cDNA libraries from the subtracted λZAP cDNA libraries were obtained by in vivo excision following the manufacturer's protocol (Stratagene) and the plasmids were isolated with Qiagen columns (Qiagen, Chatsworth, Calif.).

[0196] RSDD methodology. The purified plasmids of reciprocally subtracted cDNA libraries were directly subjected to differential display as in Liang et al. (28) with minor modifications. The plasmids of reciprocally subtracted cDNA libraries were PCR-amplified with the combination of three single-anchor 3′ primers (T₁₃A, T₁₃C or T₁₃G) and 18 arbitrary 5′ 10-mer primers obtained from Operon Technology Inc. (Alameda, Calif. OPA 1-20 except OPA1 and 3). The 20 μl PCR reaction consisted of 10 mM Tris-HCl (pH 8.4), 50 mM KCl, 1.5 mM MgCl₂, 2 μM each DNTP, 0.2 μM 5′ arbitrary primer, 1 μM 3′ anchor primer, 50 ng of plasmid of a subtracted library, 10 μCi α-³⁵S-dATP (3,000 Ci/mmol from Amersham) and 1 unit of Taq DNA polymerase (Gibco/BRL). The parameters of PCR were 30 sec at 95° C., 40 cycles of 30 sec at 95° C., 2 min at 40° C. and 30 sec at 72° C. and additional 5 min. at 72° C. After the cycling, 10 μl of 95% formamide, 0.056 bromophenol blue and 0.05% xylene cyanol were added to each PCR reaction. The mixture was heated at 95° C. for 2 min and separated in a 56 denaturing DNA sequencing gel maintained at 50° C. PCR reactions of plasmids from each subtracted library in a primer set were run side by side. Differentially amplified bands from plasmids of each subtracted library were marked with 18 G needle. through the film and cut out with a razor. The gel slice was put in 100 μl TE (pH 8.0) and incubated at 4° C. overnight. After the incubation, the mixture was boiled for 5 min and microcentrifuged for two min. The supernatant was collected and stored at −20° C. until reamplification. The band extract was reamplified with the same cycling parameters in a 50 μl reaction consisting of 10 mM Tris-HCl (pH 8.4), 50 mM KCl, 1.5 mM MgCl₂, 20 μM each dNTP, 0.2 μM 5′ arbitrary primer, 1 μM 3′ anchor primer, 5 μl of band extract and 2.5 units of Taq DNA polymerase (Gibco/BRL).

[0197] Reverse Northern Blotting Procedure. Differential expression of the reamplified DNA fragment was scrutinized by reverse Northern and Northern blot analyses. In reverse Northern analysis, after confirmation in a 1% agarose gel, the reamplified DNA fragment (10 μl of PCR reaction) was mixed with 90 μl TE and spotted on a positively charged Nylon membrane (Boehringer Mannheim) with a 96-well vacuum manifold. The membrane was soaked with denaturing and neutralizing solution successively, and the spotted DNA was crosslinked to the membrane with a UV crosslinker (Stratagene). ³²P-labeled first strand cDNA was prepared by reverse transcription of total RNA. After heating at 70° C. for 10 min and quenching on ice for two min, 0.4 μM each T₁₃A, T₁₃G and T₁₃C and 10 μg total RNA mixture was added with 50 mM Tris-HCl, (pH 8.3), 75 mM KCl, 3 mM MgCl₂, 10 mM DTT, 0.5 mM DATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.02 mM dCTP, 0.5 μl RNase inhibitor (Gibco/BRL), 100 μCi dCTP (3,000 Ci/mmol from Amersham) and 200 units Superscript RT II (Gibco/BRL) in a final 25 μl reaction. The reaction mixture was incubated at 42° C. for one hour and at 37° C. for 30 min after addition of 2 μl of RNase H (10 units, Gibco/BRL). The membrane was hybridized at 42° C. overnight in a 50t formamide hybridization solution. The hybridized membrane was washed at room temperature for 15 min with 2×standard saline citrate containing 0.1% SDS twice and at 55° C. for at least one hour with 0.1×Standard Saline Citrate containing 0.1% SDS, successively. The membrane was probed with the ³²P-labeled cDNA of E11, striped off and probed with ³²P-labeled cDNA of E11-NMT. The signal intensity of each spot was normalized against that of glyceraldehyde-3-phosphate dehydrogenase and compared between E11 and E11-NMT. Reamplified DNA fragments displaying differential expression levels ≧1.8-fold higher between the two cell types were selected and analyzed by Northern bloting analysis.

[0198] Northern Blotting Analysis. In Northern blot analysis, 10 μg of total RNA from E11 and E11-NMT cells were run side-by-side in a 1% agarose gel with formaldehyde and transferred to a positively charged Nylon membrane. Reamplification reaction (5 μl) was ³²P-labeled with a multiprime labeling kit (Boehringer Mannheim) used to probe the membrane as described above. DNA fragments expressed differentially between E11 and E11-NMT in Northern blot analyses were cloned into the EcoRV site of the pZEro-2.1 cloning vector (Invitrogene) and sequenced.

[0199] To confirm differential expression, the cloned cDNA fragment was released by EcoRI-XhoI, ³²P-labeled and used to probe Northern blots as described above. Samples of RNAs from various E11 and E11-NMT derivatives displaying either a progressed or suppressed progression phenotype, based on nude mice tumorigenesis and soft agar cloning assays were analyzed. These included E11, E11-NMT, CREF ×E11-NMT F1 and F2 somatic cell hybrids (suppressed progression phenotype), CREF×E11-NMT R1 and R2 somatic cell hybrids (progression phenotype), E11×E11-NMT A6 somatic cell hybrid (suppressed progression phenotype), E11×E11-NMT A6TD tumor-derived somatic cell hybrid (progression phenotype), E11×E11-NMT 3b somatic cell hybrid (suppressed progression phenotype), E11×E11-NMT IIa (progression phenotype), E11-NMT AZA B1 and C1 5-azacytidine treated E11-NMT clones (suppressed progression phenotype), E11-Ras R12 clone containing the Ha-ras oncogene (progression phenotype) and E11-HPV E6/E7 clone containing the human papilloma virus-18 E6 and E7 gene region (progression phenotype). Differential expression of the PEGen and PSGen genes in the various cell types was confirmed using ³²P-labeled probes and northern hybridization analysis. After reconfirmation of differential expression, the plasmids containing the differentially expressed DNA fragments were sequenced by the dideoxy sequencing procedure.

[0200] Results and Discussion

[0201] Subtraction hybridization provides a direct means of enriching for unique cDNA species and eliminating common sequences between complex genomes(7,18). DDRT-PCR is a proven methodology for the rapid identification and cloning of differentially expressed sequences between cell types (1,2,28). In principle, subtraction hybridization combined with DDRT-PCR should reduce band complexity which often obscures the identification of differentially expressed genes and generates false positive signals (21,29). RSDD has been used to analyze genes differentially expressed during transformation progression (FIG. 28). Differential RNA display was directly performed with reciprocally subtracted cDNA plasmid libraries (E11 minus E11-NMT and E11-NMT minus E11) that had not been subjected to PCR. Three single anchored oligo dT 3′ primers were used for subsequent amplification prior to display. To further streamline the DDRT-PCR procedure, reamplified cDNAs identified using RSDD were analyzed using the reverse Northern blotting procedure (30,31). cDNAs displaying differential expression by reverse Northern blotting were subsequently confirmed for true differential expression by Northern analysis.

[0202] The differential RNA display pattern of E11 and E11-NMT cells using standard differential RNA display (DDRT-PCR) and RSDD is shown in FIG. 1 (Left Panel). The differential RNA display pattern of RSDD is much less complex than that of DDRT-PCR. These experiments demonstrate that subtractive hybridization prior to differential RNA display is effective in simplifying display patterns permitting the efficient identification of differentially expressed cDNAs. Since RSDD significantly reduced the number of bands displayed, single anchor oligo dT primers, that can increase band numbers, were successfully used in subsequent applications of the RSDD approach (FIG. 1; Right Panel). Using RSDD, 234 differentially displayed cDNAs in the E11/E11-NMT tumor progression model system were isolated. Hakvoort et al.(25) used a reciprocal subtraction approach to analyze gene expression changes resulting during liver regeneration following 70% hepatectomy, i.e., normal liver subtracted from partially hepatectomized regenerating liver and vice versa. Although some bands displayed apparent enrichment, the complexity of the display pattern did not show appreciable simplification. In contrast, RSDD results in a clearer delineation and simplification of differentially expressed amplified bands (FIG. 1). Although conceptually similar, RSDD is significantly more effective than the subtraction plus DDRT-PCR approach described by Hakvoort et al. (25) The reasons for the improved efficiency of RSDD versus the Hakvoort et al. (25) approach are not known. One possibility is that the differences between the experimental approaches may reflect the subtraction hybridization strategies employed. The approach of Hakvoort et al. (25) is based on the subtraction procedure described by Wang and Brown (32). This approach uses multiple rounds of PCR-amplification prior to each round of subtractive hybridization. In contrast, RSDD involves a single round of reciprocal subtraction without intermediate amplification(5,6). In this respect, the complicated display pattern observed by Hakvoort et al. (25) even after three or four rounds of subtraction might result from reduced subtraction efficiency, PCR artifacts or a combination of these problems. Increasing the number of reactions by using two-base pair anchored oligo dT primers did not reduce the complexity of displayed bands (25). In these contexts, a critical component for the successful use of RSDD involves the use of an appropriate subtraction hybridization protocol, which can efficiently reduce cDNA complexity and generate stable populations of cDNAs for analysis.

[0203] Previous studies demonstrate that different gene cloning strategies, including DDRT-PCR, subtraction hybridization and electronic display, identify distinct subsets of differentially expressed genes (18). These results suggest that a single approach for gene identification may not identify the complete spectrum of differentially expressed genes. Similarly, RSDD and DDRT-PCR do not resolve the same differentially expressed bands (FIG. 1). Unique bands identified in DDRT-PCR that were differentially expressed when analyzed by Northern blotting were not the same as those found using RSDD and vise versa (data not shown) . These results are not surprising, since, as indicated above, subtraction hybridization and differential RNA display identified distinct differentially expressed genes (18). Apparently, specific differentially expressed genes are lost during subtraction hybridization and differential RNA display of subtracted cDNAs. On the basis of these considerations, it will be essential to use multiple gene discovery approaches to identify and clone the complete spectrum of differentially expressed genes.

[0204] DDRT-PCR can generate large numbers of differentially displayed bands making subsequent analysis both labor intensive and a daunting challenge. In order to reduce these limitations of DDRT-PCR, RSDD has been used in combination with reverse Northern analyses of isolated cDNAs. Gel extracted cDNA fragments were reamplified, dot-blotted on Nylon membranes and successively probed with reverse transcribed ³²P-cDNA from E11 or E11-NMT RNAs (FIG. 2). Signals were detected in 181 reamplified bands out of 234 (77%).

[0205] The signal intensities of the various cDNAs in reverse Northern analysis were quantified and normalized against that of GAPDH, which remained unchanged in E11 and E11-NMT cells. Progression elevated gene-3 (PEG-3) (6) was used as an additional control, to verify increased expression in E11-NMT versus E11 cells. In the reverse Northern analyses, PEG-3 levels were 4-fold higher in E11-NMT than in E11 cells, which coincided with Northern blotting results, thereby demonstrating the concordance of reverse Northern and Northern assays. A≧1.8-fold differential cut-off (after normalization for GAPDH expression) was used to identify and isolate cDNA bands displaying modified expression in E11 versus E11-NMT cells. This resulted in the identification of 7 cDNAs with higher expression in E11 versus E11-NMT cells and 65 cDNAs with elevated expression in Eli-NMT versus E11 cells. These results suggest that tumor progression in E11-NMT cells correlates with increased expression of a large number of genes, whereas only a smaller subset of genes display decreased expression.

[0206] A problem frequently encountered in DDRT-PCR, that is reduced but still can occur in RSDD, is the isolation of multiple cDNA species from what appears to be a single amplified band. When this occurs, these multiple species can produce spurious results when analyzed by reverse Northern analyses. For example, if two distinct species are isolated, one displaying modified expression and a second not displaying modified expression, an accurate estimate of differential expression will not be obtained by reverse Northern analysis. In this case, a number of potential false positives generated using reverse Northern analyses, may in reality not be false positives, but instead may represent multiple cDNAs. By performing single strand conformational polymorphism (SSCP) or reverse Northern analyses using cloned cDNA populations (33,34) this problem can be ameliorated.

[0207] The expression pattern of representative RSDD-derived cDNAs in E11 versus E11-NMT and in a more expanded E11/E11-NMT progression cell culture series is shown in FIGS. 29 and 30, respectively. Reverse Northern results correlated well with Northern blots using E11 and E11-NMT (^(˜)75% concordance) or a larger panel of cells differentially displaying the progression phenotype, including progression negative E11, CREF×E11-NMT F1 and F2, E11×E11-NMT A6, E11×E11-NMT 3b, E11-NMT Aza B1 and Aza C1 cells, and progression positive E11-NMT, CREF ×E11-NMT R1 and R2, E11×E11-NMT A6TD, E11×E11-NMT IIa, E11-Ras R12 and E11-HPV E6/E7 cells. Sequence analysis of the various PEGen cDNAs identified both unknown and known genes (Table 3). Five of 10 PEGen cDNAs (50%) were classified as novel sequences since no matches were found in current DNA databases. Novel PEGen cDNAs include, PEGen 13, 14, 24, 28 and 32. Known PEGen genes included PEGen 7 (human papilloma virus-16 early region 1 binding protein; HPV16 E1BP), PEGen 8 (phosphofructokinase kinase C; PFK-C), PEGen 21 (a fibroblast growth factor-4 inducible gene; FIN 14), PEGen 26 (poly ADP-ribose polymerase) and PEGen 30 (rat esp1 homology). In the case of the PSGen cDNAs, six of six (100%) were novel, including PSGen 12, 13, 26, 27, 28 and 29 (Table 3). TABLE 3 PEGen and PSGen genes isolated using RSDD Nomenclature^(a) (%)^(c) Identity^(b) Homology PEGen 7 Human HPV16 E1BP  90 PEGen 8 Rat phospho- 100 fructokinase C (PFK-C) PEGen 13 Unknown Novel PEGen 14 Unknown Novel PEGen 21 Murine FIN 14  94 PEGen 24 Unknown Novel PEGen 26 Rat poly ADP-ribose 100 polymerase PEGen 28 Unknown Novel PEGen 30 Rat espl  98 PEGen 32 Novel Novel PSGen 12 Unknown Novel PSGen 13 Unknown Novel PSGen 26 Unknown Novel PSGen 27 Unknown Novel PSGen 28 Unknown Novel PSGen 29 Unknown Novel

[0208] PEGen 7 is expressed at 4-fold higher levels in E11-NMT than in E11 cells. PEGen 7 is ^(˜)98% homologous to 16E1-BP, a cDNA encoding a protein identified using the yeast two-hybrid assay that interacts with human papillomavirus type 16 E11 protein (35). 16E1-BP encodes a 432aa protein of unknown function but does contain an ATPase signature motif (Gly-X4-Gly consensus ATP binding motif at aa 179 through 186). 16E1-BP appears to be a form of TRIP13, a protein previously shown to bind thyroid hormone receptor in yeast two-hybrid assays. The role of PEGen {fraction (7/16)}E1-BP in the progression phenotype in the E11/E11-NMT progression model is not known. Additional studies are necessary to determine if this gene change is associative or causative of transformation progression.

[0209] PEGen 8 is expressed at ^(˜)3- to 4- fold higher levels in E11-NMT than in E11 cells. PEGen 8 shows 100% homology to rat phosphofructokinase C (PFK-C).(36). PFK catalyzes the rate-limiting and committed step in glycolysis, the conversion of fructose 6-phosphate to fructose 1,6-biphosphate. Three subunit isozymes of PFK have been identified, that form homo- and heterotetramers with differing catalytic and allosteric properties. PFK-M is specific for cardiac and skeletal muscle, PFK-L is expressed in many tissues but is most abundant in the liver and PFK-C is expressed in several brain regions and the anterior pituitary but not in liver, skeletal muscle, or several other human tissues. The cDNA of PFK-C isolated from a rat hypothalamic cDNA library is 2643 bp and encodes a protein of 765aa (−36). In a recent study Sanchez-Martinez and Aragon (37), demonstrated that PFK-C is the predominant form of PFK in ascites tumor cells (obtained from a transplantable mouse carcinoma of mammary origin), whereas PFK-L is most abundant in the normal mammary gland. These results suggest the interesting possibility that PFK-C might contribute to the malignant nature of specific target cells. The role presently reported of PEGen 8/PFK-C in progression in the E11/E11-NMT model remains to be determined.

[0210] PEGen 21 is expressed at −3- to 4-fold higher levels in E11-NMT than in E11 cells. PEGen 21 displays ^(˜)98% homology with the fibroblast growth factor-4 inducible gene FIN-14 (38). FIN-14 is a novel cDNA of unknown function that hybridizes with a 4.5 kb mRNA that is induced 4-fold in NIH 3T3 mouse cells following treatment with FGF-4. The induction of FIN-14 occurs late (18 hr) after treatment with FGF-4 and does not occur when cells are treated for 18 hr with FGF-4 in the presence of cycloheximide (38). These results confirm that FIN-14 encodes a late-inducible gene. Moreover, nuclear run-on assays document that FIN-14 is transcriptionally activated in NIH 3T3 cells following growth factor stimulation. Tissue distribution studies indicate expression of a single mRNA species in the kidney with low levels of expression observed in several other tissues including testis and thymus. Mouse embryogenesis studies indicate that FIN-14 expression occurs constitutively in mouse embryos between day 10.5 and 15.5. Unlike NIH 3T3, FIN-14 was constitutively expressed in PC12 cells and its level did not vary appreciably in response to growth factor stimulation. The role of PEGen 21/FIN-14 in progression in E11/E11-NMT model system is not currently known.

[0211] PEGen 26 is expressed at ^(˜)3- to 4-fold higher levels in E11-NMT than in E11 cells. This cDNA is identical to rat poly(ADP-ribose) polymerase (PARP)(39). PARP contributes to the ability of eukaryotic cells to contend with both environmental and endogenous genotoxic agents (40). PARP is a nuclear enzyme that binds to DNA breaks and then catalyzes the covalent modification of acceptor proteins with poly(ADP-ribose) (39,40). PARP activity-contributes to the recovery of proliferating cells from DNA damage and to the maintenance of genomic stability, which may be regulated by effects on chromatin structure, DNA base-excision repair and cell cycle regulation (39,40). The role of PEGen 26/PARP in mediating the progression phenotype is not currently known. However, since cancer is a progressive disease characterized by the accumulation of genetic alterations in the evolving tumor (6), it is tempting to speculate that overexpression of PEGen 26/PARP in E11-NMT may facilitate the ability of these aggressive cancer cells to maintain genomic stability during cancer progression. In this context, PEGen 26/PARP may be an integral component of progression. This hypothesis is readily testable. PEGen 30 is expressed at 2- to 3-fold higher levels in E11-NMT than in E11 cells. This cDNA displays ^(˜)98.5-*v homology to rat esp1 (41). Rat esp1 encodes a 24-kDa nuclear protein which is the rat homologue of Drosophila Enhancer of split., a gene involved in ventral ectodermal development in Drosophila (41). PEGen 30 appears to be a homologue of esp1, since the message detected in E11 and E11-NMT cells (^(˜)4 kb) is larger in size than the reported esp1 transcript (1.3 kb) (41). The role of PEGen 30/esp1 in tumor progression in E11/E11-NMT model system remains to be determined.

[0212] The PSGen cDNAs, 12, 13, 26, 27, 28 and 29, consist of sequences without homology to those in various DNA data bases. Expression of PSGen 12 and PSGen 13 cDNAs is ^(˜)3- to 4-fold higher in E11 versus E11-NMT cells (FIG. 29). It is not currently known whether these genes simply correlate with or functionally regulate the progression phenotype. The identification of full-length cDNAs for PSGen-12 and PSGen-13, as well as the other novel PSGen and PEGen cDNAs, are in progress and once isolated experiments can be conducted to directly define the role of these progression-related genes in cancer progression.

[0213] Presently demonstrated is a modified gene-identification and gene-cloning technique, RSDD, that can efficiently identify differentially expressed cDNAs. As predicted, subtractive hybridization prior to differential RNA display greatly reduces band complexity, a problem encountered in standard DDRT-PCR in which RNA samples are directly analyzed without subtraction. Unlike a previous report using subtracted cDNAs processed through successive rounds of PCR (25,42), common bands were eliminated using reciprocally subtracted cDNA libraries that had not been processed using PCR. In addition to subtraction hybridization, the discovery of differentially expressed genes was further streamlined by using reverse Northern analyses with isolated cDNAs. With 3 single anchored oligo dT primers and 18 arbitrary 5′ primers, 72 bands were identified that displayed differential expression using reverse Northern analysis. Currently, 38 cDNA species have been analyzed by Northern blotting and 31 (^(˜)82%) displayed differential expression in E11 versus E11-NMT cells. Sequence analysis of the cloned cDNA fragments revealed 16 different genes, including 11 novel genes not reported in recent DNA databases. RSDD represents a method of choice either as a more efficient and less time consuming modification of the differential RNA display strategy or as a screening methodology for identifying differentially expressed genes in reciprocally subtracted cDNA libraries. Moreover, the ability of RSDD to identify differentially expressed genes that are dissimilar to those recognized using standard DDRT-PCR or subtraction hybridization indicates that this approach will be a valuable adjunct in cloning the complete repertoire of differentially expressed gene changes occurring between complex genomes.

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0 SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 42 <210> SEQ ID NO 1 <211> LENGTH: 371 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 5, 93, 153, 199, 217, 218, 221, 247, 259, 260, 274, 333, 335, 358, 360 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 1 taaancggtg gtactgctgc acggtcctcc gggtactgga aagacatccc tttgtaaggc 60 attagcccag aaactgacca tcagactgtc aancaggtac cggtatggcc agttaattga 120 aataaacagc cacagcctat tttctaagtg gtnttcagaa agtggcaagt tggtaactaa 180 gatgttccag aagattcang acttgattga tgataannaa nctttggtgt ttgtcctgat 240 tgatgangta agcactcann ggtactcatt cttngtctgc attgcctctt gctattactg 300 cctgatccct ctcatttggt tcactgtgtc gcnanctctt ttctatggat cttttccnan 360 ccacccgttt c 371 <210> SEQ ID NO 2 <211> LENGTH: 245 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 2 gtgacgtagg gtctgttgcg tcaatggtta tagcaagtga tgctctctga ttattactgc 60 tgacaatact cggccaacaa ttcttgcata gagtgctgat aaataactat gttacaaaaa 120 ggggtggtcc ctggagaaca ttacaggctt ccctaggtaa gtgtgcaggt caggagacgg 180 catattcaat cagatggctg atagttctcc gtggttatgc accggctcca gcttgcctac 240 gtcac 245 <210> SEQ ID NO 3 <211> LENGTH: 178 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 140, 163 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 3 gcagcatgat gaatttaatg caacagtcat agcagggcaa ggggagagaa aggcagatgg 60 actatctgca tcatcaagcg agggcttgtg tcggcggcta tgtgcagaga cgagcagggc 120 gaggcactta aaagctgctn gatgaaaatc cacccaggag aantctgggc ctacgtca 178 <210> SEQ ID NO 4 <211> LENGTH: 191 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 4 tgacgtaggc ccagacttct cctgggtgga ttttcatcca gcagctttta agtgcctcgc 60 cctgctcgtc tctgcacata gccgccgaca caagccctcg cttgatgatg cagatagtcc 120 atctgccttt ctctcccctt gccctgctat gactgttgca ttaaattcat catgctgcca 180 aaaaaaaaaa a 191 <210> SEQ ID NO 5 <211> LENGTH: 124 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 5 gccataaata cactttattt cattcgaaat gcataatcac actgggagca ctccctttgg 60 agcactcctc tagcagcagg tccgaagtgc tccagcatcg tcagctggct ccaacaccta 120 cgtc 124 <210> SEQ ID NO 6 <211> LENGTH: 61 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 6 tttttttttt tttggaaaca gaataaagtg ctttattctc tggctggctc tcctacgtca 60 c 61 <210> SEQ ID NO 7 <211> LENGTH: 216 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 145 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 7 tcggcgatag cattggagca agtcttatca gcaagcaatg ttttcagtta tgtttcaaag 60 ttaagaatgg gtttaaactt gctgaacgta aagattgacc ctcaagtcac tgtagcttta 120 gtacttgctt attgtattag tttanatgct agcaccgcat gtgctctgca tattctggtt 180 ttattaaaat aaaaagttga actgcaaaaa aaaaaa 216 <210> SEQ ID NO 8 <211> LENGTH: 334 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 42, 107, 126 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 8 tttttttttt tttttttttt tttttttttt tttttttttt tngccaggct atgtctcaga 60 ctttattatt attattatta ttattattat tataaataaa acatgtnctt tcaattaggt 120 tacaanagta tttatctcca taacgcttct tcatacatcc ttagttttgg attaaagtac 180 catccacccc aactcaaact gtaaccccca gtaatcccct ctaacgtgga aatttctggt 240 ttaacaactc agttaactgc cccacaaaca gtgggaggcc gctcttgcat ggctatgcca 300 cgtaaccctt cactgcttca cttcttcgct ggct 334 <210> SEQ ID NO 9 <211> LENGTH: 136 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 9 gaccgcttgt accatccaac ttgctttgtc ttctgcagag aggaggctaa agcccttgag 60 ctggctggca ctgtactcag gccggaagcc cagctcgtcc cggttcttga caaagcaagt 120 tggatggtac aagcgg 136 <210> SEQ ID NO 10 <211> LENGTH: 316 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 10 tgccgagctg ggtattgtga cggttgataa tggcggcatc atgttgccag gtaccgggta 60 agcagacctc agagcacagc ttattgtcca gtgctttcac gctcgcgacg tcaaagtcat 120 tgttattgtc acactccatg cctagaaatg cgcatgtcct ctggccatct tcttgcacag 180 gggatctgtc ctcttcctcc atgatatcat ttccctctgc atcctgctct ccagctggaa 240 ggccagcaaa attgctgtct ggggactctg ctggggtctc ctcctcttct gaaggggccc 300 tgctagcagc tcggca 316 <210> SEQ ID NO 11 <211> LENGTH: 337 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 254, 255, 256, 305, 318 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 11 aggggtcttg atggacttgg gtcggacatc ttagtgacct gtgaattctt ctgtggaggc 60 tgagtctcac gtagccgagt ttaatatctg tgctatttac taaagtatct gccaccaaat 120 tgtaccaact catagtttta tatgaatgtt gatgagtctg tatcataaat agaattgttg 180 atacatcctt aatttgtgca atattgtatg aagaagattg ttatcaatta aaaccacgcc 240 tctttatgat cctnnnaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 300 aaccncctca aatccatngg ttctaaccca aaaccct 337 <210> SEQ ID NO 12 <211> LENGTH: 307 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 12 tttttttttt catacaccat caaaccaatt ttatttctat agcaacgttt ctcacgtctg 60 aacctgagaa taagtcacca gctcttgaca gtaaacatgg gccctatcaa attatattag 120 actcctcagt gtcccgccat gtggccttgc accaaatcaa ttagtttgag ggccaaaatc 180 ctgttgggtt tcaaataaag tgtcaggtca taaggagggg gagggactca attcatggga 240 acatttttac ctgttcaaat agataaactg aattgcccta tctgtggtca cctggatcca 300 agaccct 307 <210> SEQ ID NO 13 <211> LENGTH: 296 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 59, 101, 110, 122, 131, 133, 148, 189, 191, 198 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 13 ccctgacgat aaatggtaag gaactttttt tttttttttt tttttttttt ttttttttnc 60 gaaataaaca aacacagctt attatttggg ggaacattaa nttctataan tgaacacaaa 120 anaaaattaa nanttaatgg gggggtanaa gggactttga atctatctgg tatcatgaca 180 ttgaagcana nacctgantg accagaaaga gagagagaga gagagagaga gagagagaga 240 gagaggtttc atatgagcta gtgttacagg ctttattagt ctattagtca gggacc 296 <210> SEQ ID NO 14 <211> LENGTH: 319 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 14 aatcgggctg gatgggtgta tccggcactg tttcgtagcg gcagcaactg ggtgcttcta 60 tctgaaagcg ggcttcacaa aaactactgc gccacccgac tcgctgcggc atcgcccggt 120 ggcgagtacc gtatcgcctt tcctggtgca gaagaagtgt ttacaggagg cggtcattta 180 ccgcaatctg attctgtttt ttattctccc tggcgggtga tcgcgatcgg cagtttgaaa 240 acgatcgttg aatccacgct cgggaatgat gtggcttcgc cgccaacgct tactgacatt 300 tcatttgtac agcccgatt 319 <210> SEQ ID NO 15 <211> LENGTH: 287 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 15 gccgagctgt gtaaaaccat ctatcctctg gcagatctac ttgccaggcc actcccaggg 60 ggggtagacc ctctaaagct tgagatttat cttacagatg aagacttcga gtttgcactc 120 gacatgacca gagatgaatt caacgcactg cccacctgga agcaaatgaa cctgaagaaa 180 gcgaaaggcc tgttctgagg gtgagatgac agccacagag aggtcactgc cactagacca 240 gaaagtggat ggagatatat atttggactg gtgttttttt ctgtcag 287 <210> SEQ ID NO 16 <211> LENGTH: 344 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 208, 269, 338 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 16 atcgggctgc agattggaga caagatcatg caggtgaacg gctgggacat gaccatggtc 60 actcatgacc aggctcggaa gcggctcacc aaacgttcgg aggaagtggt ccgcctgctg 120 gtgactcggc agtctctgca gaaggccgta cagcagtcca tgctgtcata gctgtagtca 180 gcctagactt ctgcccactg accttttngg gcactgagaa cacatccacg ctctgtctgt 240 atctagttct ggcttctgct gtgtgctang ccccagctct gaggagtaac agctgatccc 300 aaaggtccaa gccaaccttc ttacccctca gcccccancc cgat 344 <210> SEQ ID NO 17 <211> LENGTH: 300 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 17 tttttttttt tttgggcaac tatgtattta ttgtgtttgg aaggcagagt gagggaggag 60 accccagcag gaagaagact gggtgcagtc tagagttcct agtcaagagt aggaaggttt 120 ctgttatacc catcatagaa cgagagaggg ggctcaatag atcatcccct ttgtctctcc 180 acggggcttc ttgagcttct caaagttctt caggatgatg tcatataaca cagcataagc 240 gttacggatc tccatgacca tcagccggat ctcctggtat tccgcctcgt ccagctcggc 300 <210> SEQ ID NO 18 <211> LENGTH: 461 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 3, 161, 181, 190, 459 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 18 aanatctgct taaaagttct ttaatttgta ccatttcttc aaataaagaa ttttggtaca 60 aattaaagaa cttttaagca gatgttttgg tgcaactaat agaaaagata aaggcagcct 120 gacatgcatg cactgcctca gtgaccagta aagtcacatg nccttgggac gtcagcttag 180 ntttatcacn gtgtcccagg ggtgcttgtc aaagagatat tctgccatgc cagattcagg 240 ggctcccatc ttgcgtaagt tggtcacgtg gtcacccagt tctttaatgg atttcacctg 300 ctcattcagg taatgcgtct caatgaagtc acataagtgg ggatcattct tgtcagtagc 360 cagtttgtga agttccagta gtgactgatt cacactcttt tccaagtgca gtgcacactc 420 cattgcattc agcccgctct cccagtcatc acggtcacnt a 461 <210> SEQ ID NO 19 <211> LENGTH: 280 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 19 tgacgtaggg ccgagagcaa caagcacaga actccttctc cagtttcacc ctgatgaagt 60 tgaggcactc ttctgcactg ggaggggcca gcctgggggc caggcacatt ggacaccacc 120 ttcccatgga ctacagcgtc aatgccattg ccttctattc ctataccttc taggggctgc 180 ccctcttccc attcagccaa cactgagtgt tgggagattt ctctttttta aaaacacatg 240 agaaaataaa tgcactttac tccctcccca aaaaaaaaaa 280 <210> SEQ ID NO 20 <211> LENGTH: 177 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 20 gtaggcaata aaatgttttc agaggtgcga aaaagctttt gttttcttaa accattctta 60 gtctctgcca cacttgacac tccgtcaaag tgagaagcga actaaagacc aactgcggtg 120 gaaaatatta tgtttatgta ataaaaaaaa atcatgtaac tgcaaaaaaa aaaaaaa 177 <210> SEQ ID NO 21 <211> LENGTH: 633 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 449, 476, 478, 520, 526, 535, 570, 573, 581, 615, 619, 628 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 21 tgccgagctg aaaacataca tccgcaccgg gttgagatag ctggccctcc gtccccgggc 60 atactctttg gataagaacc ccggccttgt taccaggtac cggagtgagc tgaaaaattt 120 accgtcgaaa tgggtgatgt cctggaaaaa atggttcacc agctgccagg cagattcttt 180 gggttccaca ttttcctgcc cacagatgtg gcagaagcgg tcaagtaatg cagcattaca 240 attgaggcag atcttttctt ttctttcctt ggagtggctc aaccagcgat tttggttaaa 300 aataatcaaa aaagcgacgg caaaactttt gttatattcc cgcctgtggc atttgaactg 360 tgcccggcaa ccgaataact tttaattttg aaaataaaat gcatactaga tttttagcgg 420 ttgcctcctg gccattgctt caggcgccng cacagcgtca gcccagtttt accacnanga 480 atatcctaag cgttgaaaca gggcacagcc gaaaaaaacn ctggcnacaa aaaanatccg 540 gacatccttt ttccaatttt gaaaccgaan gcncgcaaac naaggttctt cgggaaaaaa 600 aatcgccaaa atacncgana tcaaactntc caa 633 <210> SEQ ID NO 22 <211> LENGTH: 213 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 22 tgccgagctg gggggagttc caggaatttg tggactattt ccaggaggaa ttgaggaatc 60 tagaagtaat aagaacttca caagtagaac aacagagtta attgacctct atccttaaga 120 gttaccagag aattattaaa aaactaaaga acaatcaaag cctggtcctg tgccaccacc 180 caaaaacatg tatagcctat gtgcagctcg gca 213 <210> SEQ ID NO 23 <211> LENGTH: 679 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 5, 11, 12, 13, 16, 18, 21, 23, 30, 36, 40, 41, 48, 50, 53, 55, 56, 59, 72, 91, 92, 103, 106, 120, 123, 129, 133, 136 <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 138, 143, 153, 155, 157, 165, 168, 171, 175, 178, 180, 181, 182, 194, 200, 205, 207, 210, 213, 214, 225, 232, 244, 274, <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 281, 285, 294, 299, 313, 349, 353, 358, 360, 374, 386, 388, 411, 414, 415, 452, 482, 487, 497, 499, 513, 540, 542, 556, <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 558, 559, 563, 597, 608, 621, 647, 661, 662, 671, 675 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 23 ctcanagggc nnnttngngg ncntcatgcn ccaggntccn ncccccanan gancnnccng 60 gtaaactaca cnggagtact taagtggaca nnccacatgc ganggncaag gggatcaccn 120 tcnctcctnc agnctntncg tgnctctcct gtncntncac tgccncanaa nggangcncn 180 nnctcctatc tgtntacagn aaacntngcn ctnnctctaa gctcncccac tntgtggaaa 240 ggcnatgtgt gcgtgcctct cccctatcac ggcngtttgc naaangggga tgtnctgcnc 300 ggcgatgaag ttnggtcact ccatgtttcc cagtccnacc tgttagacna agnattgnan 360 tgtgatacga ctcnctgtaa ggggantngc ggacccagta tgtttggccc nacnnccact 420 tctttaaatg gtggctaacg gcgcttccta gnataaacac tattggtccc cccctctgca 480 gnacccntta cttccgnana aaaattgttg tcntgatccg cgacaaccac accgtctgtn 540 gnttttagtt gcaacncnna tcnctccaaa aaagtttcag aaatcttcat tttcccnggt 600 tgagcccntg acaaacccct naggatttgt cgaatgtaaa gtctccngat cttcaataaa 660 nntccaaaag nctancgat 679 <210> SEQ ID NO 24 <211> LENGTH: 1150 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 24 gcggtggtga cggtagtatg gccgcacttt atggtggcgt ggaaggggga ggcacacggt 60 ccaaagtcct tttactttct gaggatgggc agatcctggc agaagcagat ggactgagca 120 caaatcactg gctgattggc acaggtacct gtgtggagag gatcaatgag atggtggaca 180 gggctaaacg gaaggctgga gtggatcctc tggtacccct tcgaagcctg ggcttgtccc 240 tgagtggtgg ggagcaggag gatgcagtga ggctcctgat ggaggagttg agggaccgat 300 ttccctacct gagtgaaagt tacttcatca ccactgatgc agcaggttcc atcgccacag 360 ctacaccgga tggtgggatt gtgctcatct ctggaacagg ctccaactgt aggcttatca 420 accctgatgg ctctgagagt ggctgtggtg gctggggcca catgatggga gacgagggat 480 cagcctactg gattgcacac caagctgtga aaattgtgtt tgactccatt gacaacctgg 540 aagcagctcc tcatgatatt ggccatgtca agcaggccat gttcaactac ttccaggtgc 600 cagatcggct aggaatcctc actcacttgt atagggactt tgataagtcc aagtttgctg 660 gattttgtca gaaaattgca gaaggtgcac agcagggaga ccctctttcc aggttcatct 720 tcagaaaggc tggggagatg ctgggcagac acgttgtggc agtattgcca gagattgacc 780 cagttttgtt ccaaggggag cttggcctcc ccattctgtg tgtgggctca gtgtggaaga 840 gctgggagct actgaaggaa ggctttctcc tggcactgac gcagggccga gagcaacagg 900 cacagaactc cttctccagt ttcaccctga tgaagttgag gcactcttct gcactgggag 960 gggccagcct gggggccagg cacattggac accaccttcc catggactac agcgtcaatg 1020 ccattgcctt ctattcctat accttctagg ggctgcccct cttcccattc agccaacact 1080 gagtgttggg agatttctct tttttaaaaa cacatgagaa aataaatgca ctttactccc 1140 tccccaaaaa 1150 <210> SEQ ID NO 25 <211> LENGTH: 348 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 25 Gly Gly Asp Gly Ser Met Ala Ala Leu Tyr Gly Gly Val Glu Gly Gly 1 5 10 15 Gly Thr Arg Ser Lys Val Leu Leu Leu Ser Glu Asp Gly Gln Ile Leu 20 25 30 Ala Glu Ala Asp Gly Leu Ser Thr Asn His Trp Leu Ile Gly Thr Gly 35 40 45 Thr Cys Val Glu Arg Ile Asn Glu Met Val Asp Arg Ala Lys Arg Lys 50 55 60 Ala Gly Val Asp Pro Leu Val Pro Leu Arg Ser Leu Gly Leu Ser Leu 65 70 75 80 Ser Gly Gly Glu Gln Glu Asp Ala Val Arg Leu Leu Met Glu Glu Leu 85 90 95 Arg Asp Arg Phe Pro Tyr Leu Ser Glu Ser Tyr Phe Ile Thr Thr Asp 100 105 110 Ala Ala Gly Ser Ile Ala Thr Ala Thr Pro Asp Gly Gly Ile Val Leu 115 120 125 Ile Ser Gly Thr Gly Ser Asn Cys Arg Leu Ile Asn Pro Asp Gly Ser 130 135 140 Glu Ser Gly Cys Gly Gly Trp Gly His Met Met Gly Asp Glu Gly Ser 145 150 155 160 Ala Tyr Trp Ile Ala His Gln Ala Val Lys Ile Val Phe Asp Ser Ile 165 170 175 Asp Asn Leu Glu Ala Ala Pro His Asp Ile Gly His Val Lys Gln Ala 180 185 190 Met Phe Asn Tyr Phe Gln Val Pro Asp Arg Leu Gly Ile Leu Thr His 195 200 205 Leu Tyr Arg Asp Phe Asp Lys Ser Lys Phe Ala Gly Phe Cys Gln Lys 210 215 220 Ile Ala Glu Gly Ala Gln Gln Gly Asp Pro Leu Ser Arg Phe Ile Phe 225 230 235 240 Arg Lys Ala Gly Glu Met Leu Gly Arg His Val Val Ala Val Leu Pro 245 250 255 Glu Ile Asp Pro Val Leu Phe Gln Gly Glu Leu Gly Leu Pro Ile Leu 260 265 270 Cys Val Gly Ser Val Trp Lys Ser Trp Glu Leu Leu Lys Glu Gly Phe 275 280 285 Leu Leu Ala Leu Thr Gln Gly Arg Glu Gln Gln Ala Gln Asn Ser Phe 290 295 300 Ser Ser Phe Thr Leu Met Lys Leu Arg His Ser Ser Ala Leu Gly Gly 305 310 315 320 Ala Ser Leu Gly Ala Arg His Ile Gly His His Leu Pro Met Asp Tyr 325 330 335 Ser Val Asn Ala Ile Ala Phe Tyr Ser Tyr Thr Phe 340 345 <210> SEQ ID NO 26 <211> LENGTH: 800 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 26 ggcacgagct ctcctcgtcc cctcccttct ccactgcagc ctttctctta gcccgaacca 60 cttccttctt ctgcttgttc ctccctaggg cgcggaagct gagtgcaggg ttcagaccca 120 cgcggcgagc agctcttcag tgaagaagga agcaatcgga gggtcagcaa tgaacgtgga 180 gcatgaggtt aacctcctgg tggaggaaat tcatcgtctg ggttccaaaa atgccgatgg 240 gaaactgagt gtgaagtttg gggtcctctt ccaagacgac agatgtgcca atctctttga 300 aaccgttggt gggaactctg aaagcccgca aaacgaagga agattgttac gtacgcagaa 360 gagctgcttt tgcaaggtgt tcatgatgat gttgacattg tattgctgca agattaatgt 420 ggtttgcaga tctgggggta tctggtaaac tggaataatt aagttaaagg acaaacatga 480 agttccttat gtatttttat agacctttgt aaacaaaagg ggacttgttg agaagtcctg 540 tttttatacc ttggagcaaa acattacaat gtaaaaataa acaaaacctg ttattttttt 600 tttcttaaga aggtaatcgg gagacgtagg caataaaatg ttttcagagg tgcgaaaaag 660 cttttgtttt cttaaaccat tcttagtctc tgccacactt gacactccgt caaagtgaga 720 agcgaactaa agaccaactg cggtggaaaa tattatgttt atgtaataaa aaaaaatcat 780 gtaaaaaaaa aaaaaaaaaa 800 <210> SEQ ID NO 27 <211> LENGTH: 92 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 27 Met Asn Val Glu His Glu Val Asn Leu Leu Val Glu Glu Ile His Arg 1 5 10 15 Leu Gly Ser Lys Asn Ala Asp Gly Lys Leu Ser Val Lys Phe Gly Val 20 25 30 Leu Phe Gln Asp Asp Arg Cys Ala Asn Leu Phe Glu Thr Val Gly Gly 35 40 45 Asn Ser Glu Ser Pro Gln Asn Glu Gly Arg Leu Leu Arg Thr Gln Lys 50 55 60 Ser Cys Phe Cys Lys Val Phe Met Met Met Leu Thr Leu Tyr Cys Cys 65 70 75 80 Lys Ile Asn Val Val Cys Arg Ser Gly Gly Ile Trp 85 90 <210> SEQ ID NO 28 <211> LENGTH: 1538 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 652, 1523 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 28 gtgtggtgtg tctctcagac gtccgtgaca ctttgatcct gccctgccgg cacctgtgcc 60 tctgcaacac ctgtgcagac accctgcgct accaggccaa caactgcccc atctgccggc 120 tgcccttccg ggcactgctt cagatccgag ccatgaggaa aaaattgggc cctctgtctc 180 caagcagctt taaccccatc atctcttccc agacttcgga ctctgaggaa cattcatcct 240 cagagaacat ccctgcgggc tatgaagtgg tgtctctcct ggaggccctc aatgggcccc 300 tcacctcatc cccagcggtg cctccccttc acgttcttgg agatggccac ctctcaggaa 360 tgctgccgtc ctatggcagt gatggccacc tgccccctgt taggacactg tccccccttg 420 accacctgtc tgattgcaac agccaagggc tcaaactcaa caagtctctc tccaagtcca 480 tttcccagaa ttcttctgtg cttcacgaag aggaagatga gcgctcttgc agtgagtcag 540 acactcagct ctctcagagg ctgtcagccc agcatcctga agagggacct gatgtgactc 600 cagagagtga gaacctcacg ctgtcctcct caggggctgt tgaccagtca tnttgcacag 660 ggactccgct ctcttccacc atctcctccc cagaagaccc agccagcagc agcctggccc 720 agtcagtcat gtccatggcc tcctcccaga tcagcactga caccgtgtcc tccatgtctg 780 gctcctacat tgcacctggc acagaagaag aaggagaggc cccaccttcc ccccgagctg 840 ctagcagggc cccttcagaa gaggaggaga ccccagcaga gtccccagac agcaattttg 900 ctggccttcc agctggagag caggatgcag agggaaatga tatcatggag gaagaggaca 960 gatcccctgt gcaagaagat ggccagagga catgcgcatt tctaggcatg gagtgtgaca 1020 ataacaatga ctttgacgtc gcgagcgtga aagcactgga caataagctg tgctctgagg 1080 tctgcttacc cggtacctgg caacatgatg ccgccattat caaccgtcac aatacccagc 1140 gccggcgact atcacccagc agcctggagg accctgagga ggacaggcct tgcgtatggg 1200 atcctttggc tgtctgaggg cactggcacc tgtacctggg cttcccctcc tgtccgcctt 1260 ccatctgtcc tcactggacc acaggccttc tgggcatctt caacaagaca cgtggacttt 1320 ctactctcat gaagggagga cagtgcaacc ctccaccaac ttcatctcct gtaaccatga 1380 ttcttaccct ctcagaaagt accagaagcc ttcctcctgt gggctgatgt gtgccagcca 1440 aacccagtgg gtcagctgag ctgagggtca gggctggttg tttctgtagc cttttctctt 1500 ccaaatggag accaacgaga aanaaaaaaa aaaaaaaa 1538 <210> SEQ ID NO 29 <211> LENGTH: 404 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: (1)...(404) <223> OTHER INFORMATION: Xaa = Any Amino Acid <400> SEQUENCE: 29 Val Val Cys Leu Ser Asp Val Arg Asp Thr Leu Ile Leu Pro Cys Arg 1 5 10 15 His Leu Cys Leu Cys Asn Thr Cys Ala Asp Thr Leu Arg Tyr Gln Ala 20 25 30 Asn Asn Cys Pro Ile Cys Arg Leu Pro Phe Arg Ala Leu Leu Gln Ile 35 40 45 Arg Ala Met Arg Lys Lys Leu Gly Pro Leu Ser Pro Ser Ser Phe Asn 50 55 60 Pro Ile Ile Ser Ser Gln Thr Ser Asp Ser Glu Glu His Ser Ser Ser 65 70 75 80 Glu Asn Ile Pro Ala Gly Tyr Glu Val Val Ser Leu Leu Glu Ala Leu 85 90 95 Asn Gly Pro Leu Thr Ser Ser Pro Ala Val Pro Pro Leu His Val Leu 100 105 110 Gly Asp Gly His Leu Ser Gly Met Leu Pro Ser Tyr Gly Ser Asp Gly 115 120 125 His Leu Pro Pro Val Arg Thr Leu Ser Pro Leu Asp His Leu Ser Asp 130 135 140 Cys Asn Ser Gln Gly Leu Lys Leu Asn Lys Ser Leu Ser Lys Ser Ile 145 150 155 160 Ser Gln Asn Ser Ser Val Leu His Glu Glu Glu Asp Glu Arg Ser Cys 165 170 175 Ser Glu Ser Asp Thr Gln Leu Ser Gln Arg Leu Ser Ala Gln His Pro 180 185 190 Glu Glu Gly Pro Asp Val Thr Pro Glu Ser Glu Asn Leu Thr Leu Ser 195 200 205 Ser Ser Gly Ala Val Asp Gln Ser Xaa Cys Thr Gly Thr Pro Leu Ser 210 215 220 Ser Thr Ile Ser Ser Pro Glu Asp Pro Ala Ser Ser Ser Leu Ala Gln 225 230 235 240 Ser Val Met Ser Met Ala Ser Ser Gln Ile Ser Thr Asp Thr Val Ser 245 250 255 Ser Met Ser Gly Ser Tyr Ile Ala Pro Gly Thr Glu Glu Glu Gly Glu 260 265 270 Ala Pro Pro Ser Pro Arg Ala Ala Ser Arg Ala Pro Ser Glu Glu Glu 275 280 285 Glu Thr Pro Ala Glu Ser Pro Asp Ser Asn Phe Ala Gly Leu Pro Ala 290 295 300 Gly Glu Gln Asp Ala Glu Gly Asn Asp Ile Met Glu Glu Glu Asp Arg 305 310 315 320 Ser Pro Val Gln Glu Asp Gly Gln Arg Thr Cys Ala Phe Leu Gly Met 325 330 335 Glu Cys Asp Asn Asn Asn Asp Phe Asp Val Ala Ser Val Lys Ala Leu 340 345 350 Asp Asn Lys Leu Cys Ser Glu Val Cys Leu Pro Gly Thr Trp Gln His 355 360 365 Asp Ala Ala Ile Ile Asn Arg His Asn Thr Gln Arg Arg Arg Leu Ser 370 375 380 Pro Ser Ser Leu Glu Asp Pro Glu Glu Asp Arg Pro Cys Val Trp Asp 385 390 395 400 Pro Leu Ala Val <210> SEQ ID NO 30 <211> LENGTH: 922 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 30 ggcacgaggc gccgccttcc tgctcgcgcc ctatcgccgc cttcctgctc gcgccctatc 60 gccgcctccg agtcttcctg cgccccgggc ttccgccgct tcattgattt ccgtttctcg 120 ccgctgcagc ctcctgacac ggtgatccgg gcgggccccg caggaatttt atcccctcac 180 cggcctcaca ctagtgtcgc atgtccacta tccagaacct ccaatctttc gacccctttg 240 ctgatgcaac taagggcgac gacttactcc cggcagggac tgaggactac attcatataa 300 gaatccagca gcggaacggc aggaagacgc tgaccactgt gcagggcatt gcggacgatt 360 atgacaaaaa gaaacttgtg aaagctttca aaaagaaatt cgcctgtaat gggactgtga 420 ttgaacaccc tgagtacgga gaggtcattc agcttcaagg cgaccaaagg aagaacattt 480 gccagtttct tttggaggtt ggcatcgtca aggaggagca gctgaaggtt cacggattct 540 aagatgaacc cgaacatgtg gcgagtttct taaatggttt tgttgtctaa ctcagtttgg 600 ctgcctcggg agatgattct ttacagtaaa cgacagactt tgcgtttatt aaatcattca 660 gacttccact cacgcctgca tggctacaga aaacatgggg tatgtaggct cctaagtcac 720 aaggaaatcg ccgtgaggtg gggacgaagc ccgagtccgt cctgacatgt ttccagtgga 780 aaagattttg ttctgagcgt tcatttctag tttattttca cttgattgtt aaatgttttt 840 gttgttgttt tattaaacca tgtatgttgc agcttaacaa taaaggagga aagtctgtgc 900 gtcaaaaaaa aaaaaaaaaa aa 922 <210> SEQ ID NO 31 <211> LENGTH: 113 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 31 Met Ser Thr Ile Gln Asn Leu Gln Ser Phe Asp Pro Phe Ala Asp Ala 1 5 10 15 Thr Lys Gly Asp Asp Leu Leu Pro Ala Gly Thr Glu Asp Tyr Ile His 20 25 30 Ile Arg Ile Gln Gln Arg Asn Gly Arg Lys Thr Leu Thr Thr Val Gln 35 40 45 Gly Ile Ala Asp Asp Tyr Asp Lys Lys Lys Leu Val Lys Ala Phe Lys 50 55 60 Lys Lys Phe Ala Cys Asn Gly Thr Val Ile Glu His Pro Glu Tyr Gly 65 70 75 80 Glu Val Ile Gln Leu Gln Gly Asp Gln Arg Lys Asn Ile Cys Gln Phe 85 90 95 Leu Leu Glu Val Gly Ile Val Lys Glu Glu Gln Leu Lys Val His Gly 100 105 110 Phe <210> SEQ ID NO 32 <211> LENGTH: 1856 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 32 ggcgttgcga cgtggacatg tcggcgtcgt tggtccgcgc caccgtgcgg gccgtgagca 60 agagaaaact gcaacccacg cgggcggcgc tcacgctgac cccctctgct gtgaacaaga 120 taaaacaact tcttaaagac aagcctgagc atgtgggtct gaaagtgggt gtgcggacca 180 ggggctgtaa cggcctctct tacagcctgg agtatacaaa gacaaaagga gatgctgatg 240 aagaagttat tcaagacgga gtccgagtgt tcatcgagaa gaaagcccag ctaaccctgt 300 taggcacaga gatggactat gtggaagaca aactgtccag tgagtttgtg tcaacaaccc 360 caacatcaag ggaacctgtg gctgcggtga aagctttaac gtctgaaagc tgaggactgc 420 aaactccagg agagctgggt ctgccttgga gcacaccgaa gaaatcatgt gatgtcccgt 480 gtcggaagtt agtgtgtggc tgcctcgtgg ttgagaataa agtgaagcat tgaaaatcaa 540 gccagcgtgt tagagttcca aaaacatggt gtctgttctc tgtaagacac aaatggagag 600 aacatggtgt ctgttctctg gaggacacaa actgagaaac tgttgagtcc tctgtcctgt 660 acagaaaact cctaccctgc ccttacgctg tagcctgctc tgtgctagaa ccagcttcgt 720 gaccattgct ttgctgggaa ttgaggaatg ggataacggg tgtgcacctg ggtcacagaa 780 tggcttgaga ctgtctcctg gccctgtctc acctcaggca gggcagctgt gggagcagca 840 gctgtgggag cggtgagggg acctggtttc cctcacctgt ggcgtggccc gttgcatctt 900 taccacgtgc ctgttgtcag atacctcatt tgccagcctc cagcaagctc agctatgagt 960 gccagtctca ggaggtaggg atcacgggcc tggtgtcagt ctgtcctctg gggcgtgctt 1020 catgcggttt gcttagacct ttcagttaga agcgcttgtg atgagcagcc aggtagacct 1080 gctgagagcg tggttctcag agcttctgcc cagccctcct cacaggtcac agcagacagt 1140 gctgtctgag acactcggtg aggagacatc ctgcctggcc agtgctccta ccagtttaga 1200 gactgcatta gttttctctt gaatggaagc cttgtgtaaa cccttttgtc tgaatggcca 1260 tcctgtttag agctttgaac cagtagtgtc ttccttcaga agatctgcag cagaggggtc 1320 cctctcagca cggcacctgg ggggcagaac atgcacacac ttacagttgc cagggtgcag 1380 atgctccctg cttcccagag gaagcttcta agtttcttta atgtggtcat caccagtttt 1440 ttgagccatg gttttgctgt atactacagg ccagccttga acccacaaca atcctcctgc 1500 ttccacgttc agaggcatgt gctaccacac ctgacctgga tcccaagttt ctctttaagt 1560 ggtcttgatg gacttgggtc ggacatctta gtgacctgtg aattcttctg tggaggctga 1620 gtctcacgta gccgagttta atatctgtgc tatttactaa agtatctgcc accaaattgt 1680 accaactcat agttttatat gaatgttgat gagtctgtat cataaataga attgttgata 1740 catccttaat ttgtgcaata ttgtatgaag aagattgtta tcaattaaaa ccacgcctct 1800 ttatgatcct aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaa 1856 <210> SEQ ID NO 33 <211> LENGTH: 134 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 33 Arg Cys Asp Val Asp Met Ser Ala Ser Leu Val Arg Ala Thr Val Arg 1 5 10 15 Ala Val Ser Lys Arg Lys Leu Gln Pro Thr Arg Ala Ala Leu Thr Leu 20 25 30 Thr Pro Ser Ala Val Asn Lys Ile Lys Gln Leu Leu Lys Asp Lys Pro 35 40 45 Glu His Val Gly Leu Lys Val Gly Val Arg Thr Arg Gly Cys Asn Gly 50 55 60 Leu Ser Tyr Ser Leu Glu Tyr Thr Lys Thr Lys Gly Asp Ala Asp Glu 65 70 75 80 Glu Val Ile Gln Asp Gly Val Arg Val Phe Ile Glu Lys Lys Ala Gln 85 90 95 Leu Thr Leu Leu Gly Thr Glu Met Asp Tyr Val Glu Asp Lys Leu Ser 100 105 110 Ser Glu Phe Val Phe Asn Asn Pro Asn Ile Lys Gly Thr Cys Gly Cys 115 120 125 Gly Glu Ser Phe Asn Val 130 <210> SEQ ID NO 34 <211> LENGTH: 1925 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 34 acgagctgaa ggtcacttcg cgcacgggtt ggacctgggg caggttggag gagtaggagt 60 atgtcattgg gcgcgaagac ggggtctggg gcaaaaaaga agggaggctg gagaaatctg 120 gacccgagac gtagtaagta caacttggca aatacatgtt agaggagcag ggaccacgct 180 catcaaaatc catcattggg ctaccttggg ctctccgcag tagccgagct taacatgatt 240 ctccactgca gctgcctctt tgaagcggat ccgtgaagta gaaatttgga gacgtaagct 300 gacgtggaaa tctatcccca tccttagcag ggaggtgctg gtcatgtgac ccgatgttga 360 aattgacaag ccgcgagcta gtcccggctt ttttttttta acccccctcc ctttcctttt 420 ttccccctcc cctccctcct cggcttcctt tctttgtagc cacctcaggg gaagcaacag 480 atcgtcactc ggtgttctca ccgaaagcac gtaatcgccg gtgtaactca tgttggctgg 540 ggggcctccc cgctcgcaga aaggctgggg tgcgccccca agcagctttc ctttgctcag 600 ctgcatggtc ctggtccacg agcgctctga gggcggcaag agagcgcaac tcctgacgcc 660 tccccccact ccccggtggg tgagggatgc tctgggatgg gggtggccag gtgaacgccc 720 ggaattgtgt agcttcaggt tccggagtct gttgtccgaa ggcttacgtt cagcaccttc 780 ttcgcagtcc ccctcccaca gacttgctct ggaaagcacc tcagtctcag aatctggctg 840 gaccccattt ggggccaggc ttcgcagcca cgatgtgccg ggcttcgtgg cttgtccgat 900 ttgcacggtg acttgattac acgctctcat tcatggtcac ttccgaagcg ctttagtgcc 960 ttccgtcccc aaaccgccaa caggcaaagc ggctttcctc cgcggtttgt caataatccg 1020 cgctgtccgg aagggcttcg ccttacccgg gttccacctt ccctgtatct ttctgcttac 1080 ttcctcatcc cacactctgt ccttggagga accccttctc ctcgctgcct gtaggggttc 1140 ggagtgactc cacagagcca gaggcgcttc tgctcaccgg tccgcaagct gcctggtctg 1200 ctgaagctga cgaatcggga aaccatgcaa ttgaggcgaa ccttgggctg ctttagaggc 1260 gctgaggagc cttctcctgg gaggcccaag gtcgatttca gcccaccagg atctggggaa 1320 gacccaacta ggggtaagag cacaccggaa ggccaagtcc gagttccagt cctagaagag 1380 gcggctgcgg gcaaggttat gacattggcc ctggacactg gtttcccagg agctattctt 1440 tctcaagaac tccacagcac ggggctgtct ccagaaaata ctcttcaacg tttatttcct 1500 ttaatcgtca acccgcagcc ctacggcggt taatgcgaga ggccaaaaat gtttggagga 1560 agaaaaacaa aggcaggaag tggccgcggc ctgacggtgc gtgtgtgtct gtaaagaagg 1620 gagggagccg gttcaatctc ttcttttttt ccccgaattt caaggtttag gcagaccccc 1680 gtagggcctg gccgaggctc acccggcgga gcatttggag gtggccaatg agtaaggctc 1740 gtcgggctga gtttcttctg atttggtcct aaagggtata tgctagtgtc cacagcggct 1800 cctgtggctg ctgttttcct cctgtcggac taaatgtacc aagaagggag agagattgag 1860 gcaccttgcg cgctcctctc tccttccgag gtagaatatc agaataaagt gtattcaggt 1920 gccaa 1925 <210> SEQ ID NO 35 <211> LENGTH: 1195 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 35 atcgggctgt actaacagat tgtttgtaaa cagtgacaca gtgataactt ccgtgttact 60 tcttaacttt atgtttctgc tttcagatct ccctcccctt ccagaggaag ttagcgatgc 120 catagcttta atgtctgttt tagctgcaaa actcattgtt cactttctgt tagaaaatct 180 aaagcaggtg gtatgcaatt tctcttgatt tggaattctt taaaggcaag taaatttgga 240 actcctgtgt tggggggtta acggaggtag gaacccaatg gtgtgtccct aggtcgtccc 300 cgttctcgga tagcacagtc tgcatagcca tagctctcaa ttatgtcact accctaatca 360 tcgcagcccg gttctcacgg actctttgaa gtcccaaaat gacttttgtt tgatcctgat 420 ttggattttc aatggaaagt aaaagcttgg ggtgaggaag cagcagctaa agcagggagt 480 tgagccagtg aattgctgac ggaaaggatt ctggtcttgg aggaggggga cctgaagcag 540 aaggaaaagg gatccttcgc ttaagttctt aggaaaaatc ttgactcaga atcccaagat 600 ttttcccttc atcccagccg ggtaaatatt tggttttgtc ttttaagtat agcatgaagc 660 ccgtggatga gagccatgtg ttgtaggatt ctcttcccta ttggctctga gcttgtgtca 720 ccgttcagtt tgctccctac aaagggacct agtttggaaa ggattggaag ggcaactgtt 780 cagcggcaat ggaacaccca aacgtggact gggacaacgg gattctgata aagggaaatt 840 tctggtctgg tcctggctgt gtcatagctc tttatgtgtg catggagagc tcttgatcca 900 agtagaatat gtaacaatac agaccaggat cttccagtca gtactgctgg gtggaagtgg 960 gcgggtgatg gtagttgcta gaagaatcat taagacagca tctgcggtga atgcgtccca 1020 aagcctcgcg gcatcagttt catctctaaa ccattagctt acagttgatt ccgtttcctg 1080 ggacagagaa acatccccac gcgaagtgac tgtgttgtgt attcatagca ctgcaaataa 1140 attcacgcgc catgatgaaa ccttgcaaat acgctttgac caaaaaaaaa aaaaa 1195 <210> SEQ ID NO 36 <211> LENGTH: 1149 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 36 gggtgtgggg cagctgggtg ggagcagcgt gcaggctacc agcaccaagt ggtgtgcctc 60 tccgggggtg tgtgcagaag gctcctgggg aaaactgcac aggtaccacc cctagacaga 120 aatcgaaaac ccacttctct cggtgcccca agcaatacaa gcattactgc atccatggga 180 gatgccgctt cgtgatggac gaacaaactc cctcctgcat ctgtgagata ggctactttg 240 gggcccggtg tgagcaggtg gacctgtttt atctccagca ggacaggggg cagatcctgg 300 tggtctgctt gataggcgtc atggtgctgt tcatcatttt agtcattggc gtcttgcacc 360 tgctgtcatc ctcttcggaa acatcgcaaa aagaagaagg aagagaaaat ggaaactttg 420 agtaaagata aaactcccat aagtgaagat attcaagaga ccaatattgc ttaacttaat 480 gattataaag ttaccacaag ctgatggcga gctccaaaag acctgactca tttgcagatg 540 gacaggacat gtctcaggaa aacagcttgc agaaatgaat gtttaaatat tgtatttgct 600 ttttcatttt atttgtaact gtgtgttgtt attgttttta ataatgatat ttttgttaca 660 gtctgatagc tgagaaaaaa atgacctggt taggtgacga caataaggga cattgaatat 720 aaactttgtt gctaggatta ttaaacaaac aaaatttgga aagaagttag attttaagaa 780 ctgagtcatg gtcaggcagc gatggcacac atctttaatc ccagcacttg ggagcagagg 840 caggtagatc tctgggagtt tgaggtcagc ctggtctaca aagcaagatc cagggtagcc 900 aaggttatat agagaaaccc tgtctcacaa aaccaaacca accaatcaac caaacagcaa 960 aacacctgag tcgataaaag ggctccccag gtttatacac ttaccgtatg ctaagagctt 1020 gaaatatatt gtttcgtttt atcgttcagt agtctgtgag attgcatttt ttctcattcc 1080 tatatataaa aaagttaaat gatttccctt agatgtagag atagaggaag ttagcgatgc 1140 catagcttt 1149 <210> SEQ ID NO 37 <211> LENGTH: 717 <212> TYPE: PRT <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 37 Asn Thr Cys Asn Asn Cys Thr Thr Asn Asn Cys Asn Asn Asn Gly Gly 1 5 10 15 Cys Thr Gly Ala Thr Ala Thr Cys Asn Gly Gly Cys Asn Cys Thr Thr 20 25 30 Cys Asn Thr Cys Cys Asn Cys Gly Ala Thr Cys Asn Cys Ala Gly Ala 35 40 45 Thr Ala Cys Asn Asn Gly Cys Asn Cys Ala Cys Cys Gly Gly Asn Asn 50 55 60 Asn Thr Asn Thr Cys Asn Gly Asn Gly Gly Thr Asn Ala Thr Cys Asn 65 70 75 80 Thr Cys Cys Asn Cys Cys Ala Thr Cys Thr Cys Thr Cys Asn Thr Cys 85 90 95 Cys Cys Cys Gly Ala Cys Asn Thr Gly Cys Ala Cys Thr Cys Cys Gly 100 105 110 Gly Gly Thr Asn Thr Asn Asn Thr Ala Cys Ala Cys Asn Gly Gly Ala 115 120 125 Cys Ala Cys Thr Gly Thr Ala Thr Cys Asn Asn Ala Cys Ala Gly Asn 130 135 140 Ala Ala Ala Cys Cys Thr Asn Cys Cys Cys Asn Gly Gly Cys Cys Cys 145 150 155 160 Cys Ala Gly Gly Gly Ala Thr Cys Ala Cys Cys Ala Thr Asn Cys Cys 165 170 175 Thr Cys Gly Asn Cys Cys Cys Asn Gly Cys Asn Thr Gly Thr Asn Thr 180 185 190 Ala Thr Ala Ala Asn Ala Thr Cys Ala Gly Gly Asn Asn Asn Thr Ala 195 200 205 Cys Ala Thr Cys Asn Ala Asn Gly Ala Ala Cys Asn Asn Ala Cys Thr 210 215 220 Ala Thr Cys Ala Cys Asn Gly Asn Thr Cys Thr Cys Thr Asn Thr Thr 225 230 235 240 Asn Asn Cys Thr Cys Ala Gly Thr Gly Thr Asn Cys Ala Cys Cys Thr 245 250 255 Thr Cys Cys Ala Cys Thr Asn Cys Asn Gly Ala Ala Asn Cys Thr Asn 260 265 270 Asn Thr Cys Gly Cys Thr Asn Cys Asn Cys Cys Asn Cys Asn Gly Thr 275 280 285 Thr Gly Gly Gly Ala Ala Ala Gly Gly Cys Gly Ala Asn Cys Asn Gly 290 295 300 Thr Asn Cys Cys Gly Gly Cys Asn Ala Cys Ala Thr Gly Cys Cys Gly 305 310 315 320 Thr Thr Thr Asn Cys Gly Asn Cys Asn Thr Cys Thr Gly Asn Asn Cys 325 330 335 Ala Cys Asn Thr Gly Gly Gly Gly Ala Thr Cys Thr Asn Cys Thr Asn 340 345 350 Cys Ala Ala Asn Gly Asn Ala Ala Thr Cys Ala Ala Thr Thr Asn Gly 355 360 365 Asn Gly Thr Ala Ala Cys Cys Cys Ala Cys Gly Gly Thr Thr Thr Asn 370 375 380 Cys Asn Cys Ala Ala Thr Cys Ala Cys Thr Ala Cys Thr Thr Cys Thr 385 390 395 400 Cys Ala Asn Asn Cys Asn Ala Asn Gly Gly Cys Cys Asn Thr Thr Gly 405 410 415 Ala Ala Asn Thr Gly Thr Thr Ala Thr Cys Cys Cys Ala Cys Cys Ala 420 425 430 Cys Cys Ala Asn Gly Gly Gly Gly Cys Asn Ala Asn Thr Cys Gly Gly 435 440 445 Gly Ala Cys Cys Thr Asn Ala Cys Ala Ala Thr Thr Cys Ala Thr Cys 450 455 460 Cys Thr Cys Ala Gly Cys Cys Gly Gly Cys Cys Cys Cys Ala Gly Asn 465 470 475 480 Cys Thr Thr Ala Ala Ala Ala Ala Ala Thr Thr Cys Ala Ala Ala Gly 485 490 495 Gly Asn Cys Asn Cys Thr Thr Gly Cys Cys Cys Gly Cys Asn Thr Thr 500 505 510 Asn Thr Thr Asn Cys Cys Thr Thr Ala Gly Cys Cys Cys Gly Cys Cys 515 520 525 Asn Cys Cys Asn Gly Ala Cys Ala Ala Cys Ala Asn Cys Cys Asn Ala 530 535 540 Asn Asn Ala Ala Cys Ala Ala Cys Cys Cys Cys Cys Asn Asn Thr Cys 545 550 555 560 Thr Thr Ala Asn Gly Thr Thr Gly Cys Asn Asn Ala Asn Cys Cys Cys 565 570 575 Ala Cys Ala Gly Gly Ala Asn Asn Thr Thr Gly Asn Asn Ala Thr Ala 580 585 590 Cys Cys Gly Gly Gly Thr Thr Thr Cys Cys Cys Cys Asn Gly Ala Ala 595 600 605 Ala Cys Thr Asn Cys Thr Cys Ala Ala Asn Gly Cys Cys Asn Cys Cys 610 615 620 Gly Thr Thr Cys Cys Ala Ala Cys Cys Cys Cys Cys Gly Thr Thr Ala 625 630 635 640 Cys Gly Ala Ala Ala Cys Cys Gly Thr Asn Cys Cys Cys Asn Thr Thr 645 650 655 Thr Cys Cys Thr Thr Cys Cys Gly Ala Gly Asn Thr Thr Gly Cys Cys 660 665 670 Thr Ala Thr Thr Ala Ala Asn Asn Cys Cys Cys Cys Cys Asn Ala Ala 675 680 685 Gly Thr Thr Cys Thr Asn Cys Thr Thr Cys Gly Thr Thr Asn Gly Asn 690 695 700 Thr Thr Cys Cys Thr Cys Cys Gly Ala Ala Ala Asn Gly 705 710 715 <210> SEQ ID NO 38 <211> LENGTH: 235 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 10, 11, 12, 13, 18, 20, 29, 30, 31, 39, 40, 46, 47, 49, 58, 71, 84, 90, 103, 111, 123, 126, 139, 141, 165, 185, 192, 199 <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 204, 211, 213, 214, 228 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 38 tcactgggcn nnntggtngn cgtcatgcnn naggttccnn cccccnnang aacctccngg 60 taatctacac nggagtctta agtngacaan cccacactgc ganggtcaag nggatcacca 120 tcnccncctc ccaagcttnt ncattgatgc tctctctgtt ccgtnccctg ccgctacaca 180 tggangctct tnctccttnt ctcntcttac nanncaaaca ttgccctntc tcata 235 <210> SEQ ID NO 39 <211> LENGTH: 328 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 6, 11, 12, 28, 37, 40, 50, 68, 74, 86, 89, 93, 101, 107, 117, 145, 159, 163, 164, 169, 172, 178, 179, 184, 186, 191 <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 192, 203, 204, 205, 215, 218, 219, 228, 229, 232, 233, 235, 237, 239, 245, 247, 248, 250, 252, 254, 266, 274, 279 <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 284, 288, 290, 300, 304, 312, 317, 322 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 39 gggaanggga nnaaaaagga attttttngg ggggggnttn tctgggaaan tttttttttt 60 tttttggnaa aaangggggg ggaaanaanc cgnttttccc naaaacnggg gggaacnggc 120 cgggggggga aaaaaaaggg ttacnaaggg aaacctttna aannggaang gntttgcnnc 180 cctntngaaa nntttgcccc ccnnnaggaa tcccnggnna aacccaannc cnncncncng 240 ggggncnntn cnangggacc ccaacncggg cccnaactng gggnaaanan gggcaaaacn 300 ggtncccggg gnaaaanggt ancccctc 328 <210> SEQ ID NO 40 <211> LENGTH: 196 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 40 tgccgagctg ggggtgaagc accggaaaac aaccgatcca tctcttatca cagggtctcc 60 aagatcccaa acccaaaagc cacattgtta attagccttt ttattgtgtt tttttttttt 120 tttttttttt tttttttttt tttttttttt tttttttttt tttttttttt tttttttttt 180 ttttggcagc tcggca 196 <210> SEQ ID NO 41 <211> LENGTH: 422 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <400> SEQUENCE: 41 tacgggcgct gatttttacg aacattacct ggcaggggaa atttgataag tatccactgt 60 gggtggcgac tacctggtaa aagacaaacc ccgtgtgaaa aggccctgga ctttttggca 120 acacaacgaa accggccacg tgaatggcat ccggtcttat gtggacttca atgttttcaa 180 cggggacagc acagattttg ccgaactatt aatgaaataa tgcagaattt cgcttttcaa 240 ataagcccat ggatcctgac gtaaaatatt tcctgctggt gatcgtgcag tccatttcga 300 tgctcatact ttggctgatg ctcaacatga cctttgggat ctattttaat tttgctttcc 360 ccgacaatgg tttgacgctt ggcaacatca tttattacct cttcctgctg ggcagctcgg 420 ca 422 <210> SEQ ID NO 42 <211> LENGTH: 304 <212> TYPE: DNA <213> ORGANISM: rattus norvegicus <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 2, 7, 71, 80, 87, 88, 92, 97, 98, 99, 103, 109, 110, 130, 133, 141, 147, 150, 159, 162, 165, 169, 172, 174, 179, 182 <223> OTHER INFORMATION: n = A,T,C or G <220> FEATURE: <221> NAME/KEY: unsure <222> LOCATION: 184, 190, 194, 195, 200, 202, 207, 209 <223> OTHER INFORMATION: n = A,T,C or G <400> SEQUENCE: 42 tncatangcc ctgaggtggg gacgaagccc gagtccgtcc tgacatgttt ccagtggaaa 60 agattttgtt ntgagcgttn ctttctnntt tnttttnnnt tgnttgttnn atgtttttgt 120 tgttgttttn ttnaaactgt ntgttgncan ttcaacatna anggnaggna antntgtgnc 180 tncnttgcan tgtnncatgn tncccananc ccaaaaaaaa aaaaaaaaaa aaaaagagta 240 caaatatcac aaaatttgac atttttgtaa taatactttg gttgttgttt ggtgacggcg 300 attg 304 

What is claimed is:
 1. A method for identifying differentially expressed nucleic acids between two samples, comprising: a. selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; b. performing reciprocal subtraction between the nucleic acid samples to produce two subtracted nucleic acid samples; c. amplifying the two subtracted nucleic acid samples; and d. comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.
 2. A method for identifying differentially expressed nucleic acids between two samples, comprising: a. selecting a first and second nucleic acid sample, wherein the nucleic acid samples contain a repertoire of nucleic acids; b. amplifying the two nucleic acid samples; c. performing reciprocal subtraction between the amplified nucleic acid samples to produce two subtracted nucleic acid samples; and d. comparing the two subtracted nucleic acid samples to identify differentially expressed nucleic acids.
 3. The method of claim 2, wherein the two subtracted nucleic acid samples from step c are amplified prior to the comparing of step d.
 4. The method of claim 1 or 2, wherein the each of the nucleic acid samples comprises a library of nucleic acids.
 5. The method of claim 1 or 2, wherein the nucleic acid samples are mRNA or cDNA derived from mRNA.
 6. The method of claim 1 or 2, wherein the nucleic acid samples are obtained from total RNA from E11 and E11-NMT cells.
 7. The method of claim 1 or 2, wherein the first and second nucleic acid samples are obtained from cells that differ in their exposure to external factors or in their gene expression.
 8. The method of claim 1 or 2, wherein the first and second nucleic acid samples are obtained from cells in different developmental stages.
 9. The method of claim 1 or 2, wherein the amplifying of step (d) comprises PCR amplification.
 10. The method of claim 9, wherein the PCR amplification uses a set of random primers.
 11. The method of claim 9, wherein the 3′ primer used in the PCR amplification is a single anchor oligo dT 3′ primer.
 12. The method of claim 9, wherein the 5′ primer is an arbitrary primer.
 13. The method of claim 1 or 2, wherein the comparing of step (e) comprises using a gel to separate the nucleic acids from both of the libraries.
 14. The method of claim 1 or 2, further comprising PCR amplifying the first and second nucleic acid samples.
 15. The method of claim 1 or 2, further comprising reamplifying differentially expressed nucleic acids.
 16. The method of claim 1 or 2, wherein the comparing of step (e) comprises comparing the quantities of the two amplified differentially expressed nucleic acids.
 17. The method of claim 1 or 2, wherein differences in the quantities of nucleic acid between the two subtracted libraries are electronically quantified.
 18. The method of claim 1 or 2, wherein the libraries of step (b) are constructed with λ-ZAP cDNA library kits.
 19. The isolated nucleic acid identified by the method of claim 1 or 2, wherein the nucleic acid was not previously known.
 20. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 12. 21. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 13. 22. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 23. 23. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 24. 24. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 25. 25. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 26. 26. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 27. 27. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 28. 28. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PSGen
 29. 29. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 13. 30. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 14. 31. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 15. 32. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 24. 33. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 28. 34. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 32. 35. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 42. 36. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 43. 37. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 44. 38. The isolated nucleic acid of claim 19, wherein the isolated nucleic acid is the nucleic acid designated PEGen
 48. 39. The isolated nucleic acid molecule of claim 19 which comprises: (a) one of the nucleic acid sequences as set forth in FIG. 35; (b) a sequence being degenerated to a sequence of (a) as a result of the genetic code; (c) a sequence encoding one of the amino acid sequences as set forth in FIG.
 35. (d) a sequence of at least 12 nucleotides capable of specifically hybridizing to the sequence of (a), (b) or (c)
 40. A purified polypeptide comprising one of the amino acid sequence as set forth in FIG.
 35. 